SEC11C

UniProt ID: Q9BY50
Organism: Homo sapiens
Review Status: COMPLETE
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Gene Description

SEC11C (SPC21, SEC11L3; EC 3.4.21.89) is a single-pass type II endoplasmic reticulum membrane protein and one of the two catalytic serine-endopeptidase subunits of the human signal peptidase complex (SPC). As the proteolytic subunit of the SPC-C paralog (with accessory subunits SPCS1, SPCS2 and SPCS3), SEC11C catalyzes cleavage of N-terminal signal (leader) peptides from secretory and membrane pre-proteins as they are translocated into the ER lumen. It belongs to peptidase family S26B and uses a Ser/His/Asp-type charge-relay catalytic system (Ser-68 nucleophile). Its active site abuts the ER membrane, where the complex locally thins the lipid bilayer, conferring selectivity for signal peptides whose hydrophobic h-region is shorter than ~18-20 residues. SEC11C is the paralog of the more broadly expressed SEC11A; the two catalytic subunits form distinct but functionally analogous SPC paralogs.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005787 signal peptidase complex
IBA
GO_REF:0000033
ACCEPT
Summary: SEC11C is the catalytic subunit of the signal peptidase complex (SPC-C paralog); membership in the SPC is its defining, conserved cellular component.
Reason: Core cellular component; SEC11C is the proteolytic subunit of the signal peptidase complex.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
Component of the signal peptidase complex paralog C (SPC-C)
GO:0008233 peptidase activity
IBA
GO_REF:0000033
ACCEPT
Summary: SEC11C is a peptidase; "peptidase activity" is a correct but generic parent of the specific serine-type endopeptidase/signal peptidase activity.
Reason: Correct general molecular function; the specific serine-type endopeptidase activity (GO:0004252) better captures SEC11C's catalytic role.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
Belongs to the peptidase S26B family
GO:0004252 serine-type endopeptidase activity
IEA
GO_REF:0000120
ACCEPT
Summary: SEC11C is a serine-type endopeptidase that uses a Ser/His/Asp charge-relay catalytic triad to cleave signal peptides; this is its core molecular function.
Reason: Core molecular function; experimentally established serine-endopeptidase (signal peptidase) activity, supported by IDA/EXP and the catalytic triad.
Supporting Evidence:
PMID:34388369
The active site is formed by a
GO:0005787 signal peptidase complex
IEA
GO_REF:0000117
ACCEPT
Summary: ARBA electronic assignment of signal peptidase complex membership, redundant with the experimental IDA evidence.
Reason: Correct core cellular component; redundant with IDA/IBA evidence.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
Component of the signal peptidase complex paralog C (SPC-C)
GO:0005789 endoplasmic reticulum membrane
IEA
GO_REF:0000044
ACCEPT
Summary: Electronic assignment of ER membrane localization from the UniProt subcellular location, consistent with the single-pass type II ER membrane topology.
Reason: Correct core localization; SEC11C is a single-pass ER membrane protein.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0008233 peptidase activity
IEA
GO_REF:0000002
ACCEPT
Summary: InterPro-based electronic assignment of peptidase activity; a generic parent of the specific serine-type endopeptidase activity.
Reason: Correct general molecular function; GO:0004252 is the informative specific term.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
Belongs to the peptidase S26B family
GO:0009003 signal peptidase activity
IEA
GO_REF:0000003
ACCEPT
Summary: EC-based electronic assignment of signal peptidase activity (EC 3.4.21.89); this is SEC11C's specific catalytic function and is experimentally supported (EXP).
Reason: Core molecular function; SEC11C is the catalytic signal peptidase of the SPC-C complex (EC 3.4.21.89).
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
EC=3.4.21.89
GO:0016020 membrane
IEA
GO_REF:0000002
KEEP AS NON CORE
Summary: SEC11C is a membrane protein; "membrane" is a correct but generic parent of the specific ER membrane localization.
Reason: Correct but generic; ER membrane (GO:0005789) is the specific and informative localization.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
Single-pass type II membrane protein
GO:0005515 protein binding
IPI
PMID:28514442
Architecture of the human interactome defines protein commun...
KEEP AS NON CORE
Summary: BioPlex (HCIP) high-throughput interactome capture; bare protein binding is uninformative for core function.
Reason: High-throughput interactome interaction; uninformative bare term not elevated to core per guidelines.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
Q9BY50; P61009: SPCS3
GO:0005515 protein binding
IPI
PMID:32296183
A reference map of the human binary protein interactome.
KEEP AS NON CORE
Summary: Binary interactome (HuRI) high-throughput capture; bare protein binding is uninformative.
Reason: High-throughput interactome interaction; uninformative bare term not elevated to core.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
Q9BY50; P61009: SPCS3
GO:0005515 protein binding
IPI
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling...
KEEP AS NON CORE
Summary: BioPlex proteome-scale interactome capture; bare protein binding is uninformative.
Reason: High-throughput interactome interaction; uninformative bare term not elevated to core.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
Q9BY50; P61009: SPCS3
GO:0005515 protein binding
IPI
PMID:34388369
Structure of the human signal peptidase complex reveals the ...
KEEP AS NON CORE
Summary: SEC11C interacts with the SPC accessory subunits SPCS2 and SPCS3 within the signal peptidase complex; the bare protein binding term is uninformative, but the SPC assembly is captured better by the signal peptidase complex part_of annotation.
Reason: Records genuine intra-complex interactions (SPCS2/SPCS3), but bare protein binding is uninformative; the functional content is captured by the signal peptidase complex CC.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
with SPCS2 and SPCS3
GO:0005515 protein binding
IPI
PMID:40205054
Multimodal cell maps as a foundation for structural and func...
KEEP AS NON CORE
Summary: Multimodal cell-map (proteomics/imaging) high-throughput capture; bare protein binding is uninformative for core function.
Reason: High-throughput interactome/cell-map interaction; uninformative bare term not elevated to core.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
Q9BY50; P61009: SPCS3
GO:0005787 signal peptidase complex
IPI
PMID:34388369
Structure of the human signal peptidase complex reveals the ...
ACCEPT
Summary: The cryo-EM structure identifies SEC11C within the assembled signal peptidase complex (SPC-C) with SPCS1/2/3; defining cellular component.
Reason: Core cellular component; SEC11C is the catalytic subunit of the structurally resolved SPC-C complex.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
Component of the signal peptidase complex paralog C (SPC-C)
GO:0005789 endoplasmic reticulum membrane
IDA
PMID:34388369
Structure of the human signal peptidase complex reveals the ...
ACCEPT
Summary: The SPC structure places SEC11C in the ER membrane, with the active site abutting the bilayer; direct experimental localization.
Reason: Core localization with direct experimental support; SEC11C acts at the ER membrane.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0016485 protein processing
IDA
PMID:34388369
Structure of the human signal peptidase complex reveals the ...
ACCEPT
Summary: SEC11C processes pre-proteins by cleaving their signal peptides; "protein processing" is a correct but generic parent of the specific signal peptide processing.
Reason: Correct biological process; the specific signal peptide processing (GO:0006465) better captures SEC11C's role.
Supporting Evidence:
PMID:34388369
it removes signal peptides (SPs) from a large
GO:0005789 endoplasmic reticulum membrane
ISS
GO_REF:0000024
ACCEPT
Summary: Sequence-similarity (ISS) transfer of ER membrane localization, consistent with the experimental IDA evidence.
Reason: Correct core localization; redundant with IDA/IEA ER membrane evidence.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0009003 signal peptidase activity
EXP
PMID:34388369
Structure of the human signal peptidase complex reveals the ...
ACCEPT
Summary: Experimental demonstration (structure + catalytic-activity/mutagenesis of the catalytic triad including Ser-68) that SEC11C is a catalytic signal peptidase of the SPC. This is the core molecular function.
Reason: Core molecular function with direct experimental support; SEC11C is a catalytic signal peptidase subunit of the SPC.
Supporting Evidence:
PMID:34388369
human SPC exists in two functional paralogs with distinct proteolytic subunits
GO:0004252 serine-type endopeptidase activity
IDA
PMID:34388369
Structure of the human signal peptidase complex reveals the ...
ACCEPT
Summary: Direct experimental demonstration of SEC11C serine-type endopeptidase (signal peptidase) activity via the resolved catalytic triad and catalytic-activity assays; core molecular function.
Reason: Core molecular function with direct experimental (IDA) support.
Supporting Evidence:
PMID:34388369
The active site is formed by a
GO:0005787 signal peptidase complex
IDA
PMID:34388369
Structure of the human signal peptidase complex reveals the ...
ACCEPT
Summary: Direct structural demonstration that SEC11C is the catalytic subunit within the assembled SPC-C; defining cellular component.
Reason: Core cellular component with direct experimental (IDA) support.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
Component of the signal peptidase complex paralog C (SPC-C)
GO:0051604 protein maturation
IDA
PMID:34388369
Structure of the human signal peptidase complex reveals the ...
ACCEPT
Summary: By cleaving signal peptides from pre-proteins, SEC11C contributes to maturation of secretory/membrane proteins; "protein maturation" is a correct but generic parent of the specific signal peptide processing.
Reason: Correct biological process; the specific signal peptide processing (GO:0006465) better captures SEC11C's role.
Supporting Evidence:
PMID:34388369
it removes signal peptides (SPs) from a large
GO:0005789 endoplasmic reticulum membrane
TAS
Reactome:R-HSA-422051
ACCEPT
Summary: Reactome curation of SEC11C ER membrane localization (preproghrelin signal peptide cleavage).
Reason: Correct core localization; redundant with experimental ER membrane evidence.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0005789 endoplasmic reticulum membrane
TAS
Reactome:R-HSA-9918795
ACCEPT
Summary: Reactome curation of SEC11C ER membrane localization (flaviviral polyprotein signalase cleavage).
Reason: Correct core localization; redundant with experimental ER membrane evidence.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane
GO:0005789 endoplasmic reticulum membrane
TAS
Reactome:R-HSA-9918871
ACCEPT
Summary: Reactome curation of SEC11C ER membrane localization (NS4B signalase cleavage).
Reason: Correct core localization; redundant with experimental ER membrane evidence.
Supporting Evidence:
file:human/SEC11C/SEC11C-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane

Core Functions

Catalytic serine-endopeptidase subunit of the ER signal peptidase complex (SPC-C paralog) that cleaves N-terminal signal peptides from secretory and membrane pre-proteins as they are translocated into the ER lumen, using a Ser/His/Asp catalytic triad.

Supporting Evidence:
  • file:human/SEC11C/SEC11C-uniprot.txt
    catalyzes the cleavage of N-terminal signal sequences
  • PMID:34388369
    The active site is formed by a

References

Gene Ontology annotation through association of InterPro records with GO terms
Gene Ontology annotation based on Enzyme Commission mapping
Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
Architecture of the human interactome defines protein communities and disease networks.
A reference map of the human binary protein interactome.
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage.
  • The human signal peptidase complex exists in two functional paralogs with distinct proteolytic subunits (SEC11A and SEC11C); the active site is formed by a catalytic triad abutting the ER membrane, where a transmembrane window thins the bilayer to generate specificity for signal peptides based on the length of their hydrophobic segments.
  • SEC11C is the catalytic subunit of SPC-C (with accessory subunits SPCS1, SPCS2, SPCS3); Ser-68 is the catalytic nucleophile and the C-terminal short (CTS) helix is essential for catalytic activity.
Multimodal cell maps as a foundation for structural and functional genomics.
The human signal peptidase complex acts as a quality control enzyme for membrane proteins.
  • Beyond canonical N-terminal signal peptide removal, the human SPC (catalytic core SEC11A/C with SPCS3) cleaves misfolded or unassembled membrane proteins at otherwise hidden "cryptic" cleavage sites abundant in the human membrane proteome; this post-translocational cleavage synergizes with ER-associated degradation (ERAD) to maintain membrane protein homeostasis. SEC11A knockdown did not abolish a noncanonical cleavage event, consistent with compensation by SEC11C.
The Natural Product Cavinafungin Selectively Interferes with Zika and Dengue Virus Replication by Inhibition of the Host Signal Peptidase.
  • Genome-wide CRISPR/Cas9 chemogenomic profiling in human cells and resistance selection in yeast identified the catalytic subunit of the signal peptidase (SEC11; human SEC11A and SEC11C) as the conserved efficacy target of cavinafungin, which rapidly blocks signal-sequence cleavage of host and viral proteins.
Spc2 modulates substrate- and cleavage site-selection in the yeast signal peptidase complex.
  • In yeast, the noncatalytic SPC subunit Spc2 (ortholog of human SPCS2) modulates SPC discrimination between substrates and cleavage-site selection; molecular dynamics indicates Spc2 contributes to the membrane thinning at the center of the SPC that underlies substrate recognition, informing the conserved mechanism by which accessory subunits support the SEC11 catalytic subunit.
Competitive Inhibition of the Endoplasmic Reticulum Signal Peptidase by Non-cleavable Mutant Preprotein Cargos.
  • A non-cleavable variant preprotein (proline introduced immediately after the signal-peptide cleavage site) is translocated across the ER membrane where it binds the catalytic SPase subunit and inhibits signal peptidase activity in a dose-dependent manner; this work directly implicates SEC11A as the catalytic subunit and establishes eukaryotic SPase as a tractable antiviral target, informing the shared catalytic mechanism of the SEC11A/SEC11C signal peptidase paralogs.
Reactome:R-HSA-422051
Cleavage of the signal peptide of Preproghrelin
Reactome:R-HSA-9918795
Signalase cleaves prM-E-NS1-NS2A
Reactome:R-HSA-9918871
Signalase cleaves prepro-NS4B
file:human/SEC11C/SEC11C-uniprot.txt
UniProt entry Q9BY50 (SC11C_HUMAN), Signal peptidase complex catalytic subunit SEC11C
  • SEC11C is the catalytic subunit of the signal peptidase complex paralog C (SPC-C) with SPCS1/2/3; cleaves N-terminal signal peptides (EC 3.4.21.89) from nascent proteins translocated into the ER lumen; single-pass type II ER membrane protein; peptidase S26B family; catalytic triad (Ser-68), selectivity for h-regions shorter than 18-20 residues via membrane thinning.

Suggested Questions for Experts

Q: What distinguishes the substrate specificity of the SEC11C (SPC-C) versus SEC11A (SPC-A) paralogous signal peptidase complexes, and do they serve distinct subsets of the secretory proteome or distinct tissues?

Q: How does the SPC's local thinning of the ER membrane mechanistically couple signal-peptide h-region length to catalytic engagement by SEC11C?

Suggested Experiments

Experiment: Reconstitute purified SPC-C (SEC11C + SPCS1/2/3) and assay cleavage of a panel of signal peptides varying in h-region length to quantify SEC11C's length-dependent specificity, comparing wild-type Ser-68 to the catalytic-dead S68A mutant.

Experiment: Acute degron depletion of SEC11C versus SEC11A followed by N-terminomics (e.g. TAILS) to define the paralog-specific repertoire of cleaved signal-peptide substrates in human cells.

Deep Research

Falcon

(SEC11C-deep-research-falcon.md)
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 22 citations 3 artifacts 2026-06-12T03:05:32.314757

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Human SEC11C (UniProt: Q9BY50) — Functional Annotation and Current Understanding

1) Gene/protein identity verification (critical)

SEC11C (UniProt Q9BY50; also referred to as SPC21/SEC11 homolog C) is a catalytic subunit of the endoplasmic-reticulum (ER) signal peptidase complex (SPC) in Homo sapiens. Multiple primary sources describing the human SPC explicitly place SEC11C as one of the two alternative proteolytic (catalytic) subunits (the other being SEC11A) that define two functional SPC paralogs (SPC-C vs SPC-A). (liaci2021structureofthe pages 3-4, liaci2021structureofthe pages 1-3)

2) Key concepts and definitions (current understanding)

2.1 Signal peptidase complex (SPC)

The SPC is an essential ER membrane protease responsible for removing signal peptides from secretory-pathway preproteins. In humans, structural and biochemical work supports that the SPC exists as two paralogous heterotetramers that differ in the catalytic SEC11 subunit. (liaci2021structureofthe pages 3-4, liaci2021structureofthe pages 1-3)

2.2 Catalytic activity (EC 3.4.21.89) and reaction

The SPC is a serine protease that hydrolyzes the peptide bond at the signal peptide cleavage site of secretory preproteins after they enter the ER lumen, i.e., signal peptide removal (EC 3.4.21.89). Structural modeling and functional assays support that SEC11C-containing SPC is catalytically active and carries the protease active site. (liaci2021structureofthe pages 1-3, liaci2021structureofthe pages 3-4)

2.3 Canonical vs noncanonical (quality-control) cleavage

Beyond canonical signal peptide cleavage, recent work shows a post-translocational “quality-control” (QC) function in which SPC can cleave cryptic/noncanonical sites in membrane proteins—particularly when proteins fail to fold/assemble properly—thereby facilitating ER-associated degradation (ERAD). (zanotti2022thehumansignal pages 1-8, zanotti2022thehumansignal pages 53-57)

3) Molecular function of SEC11C within SPC

3.1 Complex composition and paralogs

High-confidence structural proteomics indicates that the human SPC exists as two functional paralogs:
- SPC-A: SPC12 + SPC22/23 + SPC25 + SEC11A
- SPC-C: SPC12 + SPC22/23 + SPC25 + SEC11C

Both paralogs can be purified as near-stoichiometric complexes from HEK293 cells and both are enzymatically active in vitro, demonstrating that SEC11C supports an active SPC protease complex. (liaci2021structureofthe pages 3-4, liaci2021structureofthe pages 1-3)

3.2 Catalytic mechanism: serine protease triad and active-site architecture

Cryo-EM and modeling support that the SPC catalytic center (including in SEC11C) uses a Ser–His–Asp catalytic triad positioned in a c-region binding pocket that accommodates the signal peptide cleavage region and places the scissile bond near catalytic residues. (liaci2021structureofthe pages 1-3, liaci2021structureofthe pages 7-8)

Figure evidence (cropped panels) from the structural study depicts (i) SPC-A vs SPC-C paralogs and (ii) the active-site architecture and membrane-thinning context. (liaci2021structureofthe media edf6a0de, liaci2021structureofthe media e833f187, liaci2021structureofthe media 63103722, liaci2021structureofthe media d6c9aae3)

3.3 Substrate recognition and specificity (current mechanistic model)

A central mechanistic insight is that the SPC forms a transmembrane “window” that locally thins the ER bilayer near the active site. This architecture acts as a “molecular ruler” that favors the shorter hydrophobic h-regions typical of signal peptides over longer transmembrane helices, supporting specificity across many substrates. (liaci2021structureofthe pages 1-3, liaci2021structureofthe media edf6a0de)

Consistent with this model, both SEC11A- and SEC11C-containing paralogs process a model preprotein substrate (pre-β-lactamase) in vitro with similar efficiency, indicating that SEC11C supports canonical signal peptide cleavage. (liaci2021structureofthe pages 3-4)

4) Subcellular localization and topology

SEC11C functions in the ER membrane. Structural/topology inferences from digitonin-solubilized particles place the catalytic domain on the luminal side, positioned close to the membrane surface, with the C-terminus on the cytosolic side. SPCS3’s luminal domain helps stabilize and position the catalytic region of SEC11A/C near the luminal membrane interface. (liaci2021structureofthe pages 7-8, chung2024spc2modulatessubstrate pages 1-2)

5) Recent developments and latest research (emphasis 2023–2024)

5.1 2022–2023: SPC as a membrane-protein quality-control protease (human)

A major conceptual advance is that the human SPC is not only a signal-peptide-removing enzyme but also a quality-control protease for membrane proteins, cleaving cryptic sites in misfolded/unassembled membrane proteins and synergizing with ERAD to maintain membrane proteostasis. (zanotti2022thehumansignal pages 1-8, zanotti2022thehumansignal pages 53-57)

SEC11C is implicated as part of the catalytic core in this QC activity because the catalytic core is described as SEC11A/C with SPCS3, and pharmacologic inhibition of SEC11 activity blocks noncanonical cleavage. (zanotti2022thehumansignal pages 53-57, zanotti2022thehumansignal pages 26-30)

5.2 SEC11A–SEC11C redundancy and conditional abundance

Human SEC11A knockdown did not abolish cleavage of a noncanonical substrate (Cx32), and the authors propose compensation by SEC11C upregulation. However, SEC11C was reported as often difficult to detect in several cell lines when SEC11A levels are normal, suggesting SEC11C may act as a backup/conditionally expressed catalytic subunit depending on context. (zanotti2022thehumansignal pages 57-60, zanotti2023characterisationofthe pages 57-60)

5.3 2024: accessory subunit control of cleavage-site selection (mechanistic context)

A 2024 mechanistic study in yeast shows accessory subunits can modulate substrate and cleavage-site selection, and explicitly situates this in the context that higher eukaryotes have two SEC11 paralogs (SEC11A, SEC11C) within a four-subunit eukaryotic SPC. Quantitatively, the paper reports Sec11 abundance is reduced by ~10% in spc2Δ yeast, illustrating how non-catalytic subunits can affect catalytic subunit stability/assembly. (chung2024spc2modulatessubstrate pages 1-2)

6) Pathways and biological processes linked to SEC11C/SPC

6.1 Secretory-pathway protein biogenesis

SEC11C-containing SPC participates in co-/post-translational processing of proteins entering the secretory pathway by cleaving signal peptides after ER targeting/translocation. (liaci2021structureofthe pages 1-3)

6.2 ER protein quality control and ERAD coupling

The QC role links SPC cleavage to ERAD: SPC can cleave membrane proteins that fail to fold/assemble, and SPC is reported to interact functionally with the ERAD E3 ligase Hrd1, facilitating degradation of problematic membrane proteins. (zanotti2022thehumansignal pages 57-60)

7) Current applications and real-world implementations

7.1 Chemical biology and host-targeted antiviral strategies: cavinafungin

The natural product cavinafungin inhibits the host signal peptidase and selectively interferes with Zika and dengue virus replication by targeting SEC11-containing SPC activity.

Key quantitative/implementation-relevant results include:
- Dose-response metrics in HCT116 cells: IC10 = 450 nM, IC30 = 600 nM, IC50 = 710 nM (cell viability assay used for chemogenomic profiling). (estoppey2017thenaturalproduct pages 4-5)
- Genome-wide CRISPR/Cas9 chemogenomic profiling identifies signal peptidase components among top hits, including SEC11A and SEC11C and accessory subunits (e.g., SPCS3), linking drug sensitivity to the catalytic core and complex integrity. (estoppey2017thenaturalproduct pages 4-5)

In the SPC-QC context, cavinafungin (reported at 1 µM in HEK293T experiments) produces complete loss of a noncanonical SPC cleavage fragment (Cx32 C201R), establishing practical use of SPC inhibition to interrogate membrane-protein QC cleavage. (zanotti2022thehumansignal pages 26-30)

7.2 Broad translational rationale: SPC as a drug target node

Earlier biochemical work supports that inhibiting ER signal peptidase impairs maturation of secretory and viral proteins, motivating a host-targeted antiviral concept for SEC11-family catalytic subunits. (cui2015competitiveinhibitionof pages 1-2)

8) Relevant statistics and quantitative data (from recent/primary studies)

  • ~1,500 membrane proteins were identified with putative cryptic SPC cleavage sites in proteome-wide analyses (human SPC QC framework). (zanotti2022thehumansignal pages 1-8, zanotti2022thehumansignal pages 53-57)
  • A stricter filtered subset identified 262 proteins containing a cryptic cleavage site after additional filtering steps in the same study’s pipeline. (zanotti2022thehumansignal pages 26-30)
  • Cavinafungin blocks a noncanonical SPC cleavage fragment at 1 µM in a human-cell assay (Cx32 mutant). (zanotti2022thehumansignal pages 26-30)
  • Cavinafungin chemogenomic profiling in human cells used potency benchmarks of IC10 450 nM, IC30 600 nM, and IC50 710 nM. (estoppey2017thenaturalproduct pages 4-5)
  • In yeast, deletion of Spc2 reduced Sec11 abundance by ~10%, consistent with accessory-subunit effects on SPC assembly/stability. (chung2024spc2modulatessubstrate pages 1-2)
  • SPC membrane thinning near the active site was reported to reduce the bilayer thickness from ~4 nm to ~2.3 nm in structural/MD analyses. (liaci2021structureofthe media edf6a0de)

9) Expert interpretation and analysis (synthesis from authoritative sources)

9.1 SEC11C is best understood as a catalytic paralog whose specific biology may be context-dependent

The strongest direct mechanistic evidence for SEC11C comes from structural and biochemical demonstration that SEC11C defines a functional paralog (SPC-C) with an intact catalytic machinery and the same overall architecture and activity class as SEC11A-containing SPC. (liaci2021structureofthe pages 3-4, liaci2021structureofthe pages 1-3)

However, functional studies expanding SPC’s biology into membrane-protein QC emphasize potential paralog redundancy and report difficulty detecting SEC11C in some cell lines under baseline conditions—suggesting SEC11C’s contribution could vary with tissue/cell state, stress, or SEC11A availability. (zanotti2022thehumansignal pages 57-60, zanotti2023characterisationofthe pages 57-60)

9.2 Substrate scope is broader than classical signal peptides

Human SPC biology now includes both canonical signal peptides and a substantial predicted landscape of cryptic cleavage sites in membrane proteins, with validated substrates including connexins and other membrane proteins (e.g., PMP22, iRhom2, Hrd1). This reframes SEC11C-containing SPC not only as a housekeeping signal-peptide peptidase but also as a potential node in membrane-protein homeostasis. (zanotti2022thehumansignal pages 1-8, zanotti2022thehumansignal pages 53-57)

10) Limitations and evidence gaps specific to SEC11C

  • SEC11C-specific phenotypes, disease associations, and substrate preferences distinct from SEC11A were not directly quantified in the retrieved 2022–2024 human literature excerpts; instead, many findings apply to the SPC catalytic core (SEC11A/C) or to accessory subunits (notably SPCS1). (zanotti2022thehumansignal pages 57-60, zanotti2022thehumansignal pages 53-57)
  • A substantial fraction of SEC11C mechanistic detail still relies on the 2021 structural anchor (cryo-EM/proteomics/in vitro cleavage). (liaci2021structureofthe pages 7-8, liaci2021structureofthe pages 3-4, liaci2021structureofthe pages 1-3)

Embedded evidence tables

The following tables summarize the evidence base and key studies with DOI URLs and dates.

Year (month) Citation (first author et al.) Title (short) Study type Key SEC11C-relevant takeaways URL (DOI)
2015 (Nov) Cui et al. Competitive inhibition of ER signal peptidase inhibitor/antiviral Defines mammalian ER signal peptidase as a five-subunit complex including SEC11C and SEC11A; supports the catalytic importance of SEC11-family subunits and shows that blocking signal peptidase impairs maturation of secretory and viral proteins, motivating host-targeted antiviral interest (cui2015competitiveinhibitionof pages 1-2). https://doi.org/10.1074/jbc.m115.692350
2021 (Jan) Liaci et al. Human SPC structure and signal peptide cleavage determinants structure/mechanism Structural anchor for human SEC11C: shows two human SPC paralogs, SPC-A and SPC-C, each with either SEC11A or SEC11C plus SPC12/SPC22-23/SPC25; supports a Ser-His-Asp catalytic triad, luminal catalytic domain, ER-membrane-proximal active site, and local membrane thinning that helps discriminate signal peptides by hydrophobic segment length; SEC11C-containing SPC is active in vitro (liaci2021structureofthe pages 7-8, liaci2021structureofthe pages 3-4, liaci2021structureofthe pages 1-3, liaci2021structureofthe media edf6a0de). https://doi.org/10.2139/ssrn.3778304
2022 (Dec) Zanotti et al. Human SPC as membrane-protein quality control enzyme QC Expands SPC biology beyond canonical signal peptide removal: identifies a post-translocational QC role in cleaving cryptic sites in misfolded or surplus membrane proteins and coupling this to ERAD; reports ~1,500 membrane proteins with putative cryptic SPC cleavage sites and notes SEC11A knockdown can be buffered by SEC11C, implying paralog redundancy in mammalian cells (zanotti2022thehumansignal pages 57-60, zanotti2022thehumansignal pages 53-57, zanotti2022thehumansignal pages 1-8, zanotti2022thehumansignal pages 26-30). https://doi.org/10.1126/science.abo5672
2023 (Jan) Zanotti Characterisation of the human SPC as a QC enzyme QC / subunit function Thesis-level expansion of the 2022 Science study: states the catalytic core is formed by SEC11A/C with SPCS3, proposes SEC11C may serve as a backup catalytic subunit when SEC11A is limiting, and notes SEC11C is often hard to detect in some cell lines with normal SEC11A levels; cavinafungin is discussed as likely inhibiting SEC11C as well as SEC11A (zanotti2023characterisationofthe pages 57-60, zanotti2023characterisationofthe pages 53-57). https://doi.org/10.11588/heidok.00033417
2024 (Nov) Chung et al. Spc2 modulates substrate and cleavage-site selection subunit function / mechanism Although performed in yeast, this recent mechanistic study is relevant to human SEC11C because it explicitly frames higher-eukaryote SPC as a heterotetramer containing SEC11A or SEC11C and shows how accessory subunits shape substrate and cleavage-site selection, reinforcing that catalytic SEC11 paralogs act within a coordinated multi-subunit membrane-thinning machine rather than alone (chung2024spc2modulatessubstrate pages 1-2). https://doi.org/10.1083/jcb.202211035

Table: This table summarizes the main publications needed to annotate human SEC11C in context of the signal peptidase complex. It highlights the structural basis, quality-control function, subunit redundancy, and translational relevance of SEC11C/SPC across foundational and recent studies.

Claim/Topic Key findings (1-2 sentences) Evidence type Primary source (first author, journal) Pub year/month DOI URL
Identity SEC11C matches UniProt Q9BY50 as the human signal peptidase complex catalytic subunit also called SPC21; it is one of two alternative proteolytic SPC subunits, the other being SEC11A, and belongs to the conserved Sec11/S26 signal peptidase family (liaci2021structureofthe pages 7-8, liaci2021structureofthe pages 3-4, liaci2021structureofthe pages 1-3). Cryo-EM, proteomics, review/background Liaci, SSRN Electronic Journal 2021/01 https://doi.org/10.2139/ssrn.3778304
Complex composition Human SPC forms two heterotetrameric paralogs, SPC-A and SPC-C, each composed of SPC12, SPC22/23, SPC25, and either SEC11A or SEC11C; co-expression and affinity purification from HEK293 cells recovered near-stoichiometric complexes for each paralog (liaci2021structureofthe pages 3-4, liaci2021structureofthe pages 1-3, liaci2021structureofthe media edf6a0de). Cryo-EM, affinity purification, MS Liaci, SSRN Electronic Journal 2021/01 https://doi.org/10.2139/ssrn.3778304
Catalytic mechanism SEC11C is the catalytic protease of the ER SPC (EC 3.4.21.89). Structural analysis supports a Ser-His-Asp catalytic triad positioned in a c-region binding pocket adjacent to the membrane, with signal-peptide scissile bonds modeled near the catalytic residues (liaci2021structureofthe pages 7-8, liaci2021structureofthe pages 1-3, liaci2021structureofthe media edf6a0de). Cryo-EM, modeling, structural proteomics Liaci, SSRN Electronic Journal 2021/01 https://doi.org/10.2139/ssrn.3778304
Localization/topology SEC11C acts in the endoplasmic reticulum membrane with its catalytic domain exposed on the luminal side near the membrane surface, whereas its C terminus lies on the cytosolic side; the luminal domain of SPCS3 helps stabilize and position the catalytic core (liaci2021structureofthe pages 7-8, liaci2021structureofthe pages 3-4, chung2024spc2modulatessubstrate pages 1-2). Cryo-EM, topology inference, comparative analysis Liaci, SSRN Electronic Journal 2021/01 https://doi.org/10.2139/ssrn.3778304
Substrate recognition The SPC creates a locally thinned membrane window that acts as a molecular ruler favoring shorter hydrophobic h-regions typical of signal peptides over longer transmembrane helices. Both SEC11A- and SEC11C-containing complexes cleaved a pre-β-lactamase substrate with similar efficiency in vitro (liaci2021structureofthe pages 3-4, liaci2021structureofthe pages 1-3, liaci2021structureofthe media edf6a0de). Cryo-EM, molecular dynamics, in vitro cleavage assay Liaci, SSRN Electronic Journal 2021/01 https://doi.org/10.2139/ssrn.3778304
Quality-control role Beyond canonical signal peptide removal, the human SPC can cleave cryptic sites in misfolded or surplus membrane proteins, promoting their degradation and membrane proteostasis. SEC11C is part of this catalytic machinery, and the 2023 characterization proposed SEC11C may provide backup catalytic capacity when SEC11A is limiting (zanotti2023characterisationofthe pages 57-60, zanotti2023characterisationofthe pages 53-57). Cell biology, genetic/knockdown interpretation, thesis synthesis Zanotti, Science; Zanotti, thesis 2022/12; 2023/01 https://doi.org/10.1126/science.abo5672 ; https://doi.org/10.11588/heidok.00033417
Inhibitor/antiviral relevance Eukaryotic SPase is a plausible antiviral target because inhibition impairs maturation of secretory and viral proteins. Cavinafungin inhibits host signal peptidase by targeting SEC11-containing SPC, and reviews note the complex contains SEC11A and SEC11C; the 2023 thesis states cavinafungin should in principle also bind SEC11C (zanotti2023characterisationofthe pages 57-60, cui2015competitiveinhibitionof pages 1-2). Small-molecule inhibition, virology, review/background Cui, JBC; Zanotti, thesis 2015/11; 2023/01 https://doi.org/10.1074/jbc.m115.692350 ; https://doi.org/10.11588/heidok.00033417
Quantitative data Cryo-EM structures were determined at about 4.9 Å resolution for the human paralogs, and membrane thickness near the active site was reported to decrease from ~4 nm to ~2.3 nm. In yeast, loss of Spc2 reduced Sec11 abundance by ~10%, supporting accessory-subunit effects on catalytic-subunit stability (liaci2021structureofthe pages 3-4, chung2024spc2modulatessubstrate pages 1-2, liaci2021structureofthe media edf6a0de). Cryo-EM, molecular dynamics, quantitative MS Liaci, SSRN Electronic Journal; Chung, Journal of Cell Biology 2021/01; 2024/11 https://doi.org/10.2139/ssrn.3778304 ; https://doi.org/10.1083/jcb.202211035

Table: This table summarizes functional annotation evidence for human SEC11C (UniProt Q9BY50), covering identity, complex membership, catalytic mechanism, localization, substrate recognition, quality-control function, and translational relevance. It is designed to support a concise, citation-backed report using only validated context IDs from the gathered literature.

References

  1. (liaci2021structureofthe pages 3-4): A. Manuel Liaci, Barbara Steigenberger, Sem Tamara, Paulo Cesar Telles de Souza, Mariska Gröllers-Mulderij, Patrick Ogrissek, Siewert Jan Marrink, Richard Scheltema, and Friedrich Förster. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. SSRN Electronic Journal, Jan 2021. URL: https://doi.org/10.2139/ssrn.3778304, doi:10.2139/ssrn.3778304. This article has 148 citations.

  2. (liaci2021structureofthe pages 1-3): A. Manuel Liaci, Barbara Steigenberger, Sem Tamara, Paulo Cesar Telles de Souza, Mariska Gröllers-Mulderij, Patrick Ogrissek, Siewert Jan Marrink, Richard Scheltema, and Friedrich Förster. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. SSRN Electronic Journal, Jan 2021. URL: https://doi.org/10.2139/ssrn.3778304, doi:10.2139/ssrn.3778304. This article has 148 citations.

  3. (zanotti2022thehumansignal pages 1-8): Andrea Zanotti, João P. L. Coelho, Dinah Kaylani, Gurdeep Singh, Marina Tauber, Manuel Hitzenberger, Dönem Avci, Martin Zacharias, Robert B. Russell, Marius K. Lemberg, and Matthias J. Feige. The human signal peptidase complex acts as a quality control enzyme for membrane proteins. Science, 378:996-1000, Dec 2022. URL: https://doi.org/10.1126/science.abo5672, doi:10.1126/science.abo5672. This article has 41 citations and is from a highest quality peer-reviewed journal.

  4. (zanotti2022thehumansignal pages 53-57): Andrea Zanotti, João P. L. Coelho, Dinah Kaylani, Gurdeep Singh, Marina Tauber, Manuel Hitzenberger, Dönem Avci, Martin Zacharias, Robert B. Russell, Marius K. Lemberg, and Matthias J. Feige. The human signal peptidase complex acts as a quality control enzyme for membrane proteins. Science, 378:996-1000, Dec 2022. URL: https://doi.org/10.1126/science.abo5672, doi:10.1126/science.abo5672. This article has 41 citations and is from a highest quality peer-reviewed journal.

  5. (liaci2021structureofthe pages 7-8): A. Manuel Liaci, Barbara Steigenberger, Sem Tamara, Paulo Cesar Telles de Souza, Mariska Gröllers-Mulderij, Patrick Ogrissek, Siewert Jan Marrink, Richard Scheltema, and Friedrich Förster. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. SSRN Electronic Journal, Jan 2021. URL: https://doi.org/10.2139/ssrn.3778304, doi:10.2139/ssrn.3778304. This article has 148 citations.

  6. (liaci2021structureofthe media edf6a0de): A. Manuel Liaci, Barbara Steigenberger, Sem Tamara, Paulo Cesar Telles de Souza, Mariska Gröllers-Mulderij, Patrick Ogrissek, Siewert Jan Marrink, Richard Scheltema, and Friedrich Förster. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. SSRN Electronic Journal, Jan 2021. URL: https://doi.org/10.2139/ssrn.3778304, doi:10.2139/ssrn.3778304. This article has 148 citations.

  7. (liaci2021structureofthe media e833f187): A. Manuel Liaci, Barbara Steigenberger, Sem Tamara, Paulo Cesar Telles de Souza, Mariska Gröllers-Mulderij, Patrick Ogrissek, Siewert Jan Marrink, Richard Scheltema, and Friedrich Förster. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. SSRN Electronic Journal, Jan 2021. URL: https://doi.org/10.2139/ssrn.3778304, doi:10.2139/ssrn.3778304. This article has 148 citations.

  8. (liaci2021structureofthe media 63103722): A. Manuel Liaci, Barbara Steigenberger, Sem Tamara, Paulo Cesar Telles de Souza, Mariska Gröllers-Mulderij, Patrick Ogrissek, Siewert Jan Marrink, Richard Scheltema, and Friedrich Förster. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. SSRN Electronic Journal, Jan 2021. URL: https://doi.org/10.2139/ssrn.3778304, doi:10.2139/ssrn.3778304. This article has 148 citations.

  9. (liaci2021structureofthe media d6c9aae3): A. Manuel Liaci, Barbara Steigenberger, Sem Tamara, Paulo Cesar Telles de Souza, Mariska Gröllers-Mulderij, Patrick Ogrissek, Siewert Jan Marrink, Richard Scheltema, and Friedrich Förster. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. SSRN Electronic Journal, Jan 2021. URL: https://doi.org/10.2139/ssrn.3778304, doi:10.2139/ssrn.3778304. This article has 148 citations.

  10. (chung2024spc2modulatessubstrate pages 1-2): Yeonji Chung, Chewon Yim, Gilberto P. Pereira, Sungjoon Son, Lisbeth R. Kjølbye, Lauren E. Mazurkiewicz, Amy M. Weeks, Friedrich Förster, Gunnar von Heijne, Paulo C.T. Souza, and Hyun Kim. Spc2 modulates substrate- and cleavage site-selection in the yeast signal peptidase complex. Journal of Cell Biology, Nov 2024. URL: https://doi.org/10.1083/jcb.202211035, doi:10.1083/jcb.202211035. This article has 4 citations and is from a highest quality peer-reviewed journal.

  11. (zanotti2022thehumansignal pages 26-30): Andrea Zanotti, João P. L. Coelho, Dinah Kaylani, Gurdeep Singh, Marina Tauber, Manuel Hitzenberger, Dönem Avci, Martin Zacharias, Robert B. Russell, Marius K. Lemberg, and Matthias J. Feige. The human signal peptidase complex acts as a quality control enzyme for membrane proteins. Science, 378:996-1000, Dec 2022. URL: https://doi.org/10.1126/science.abo5672, doi:10.1126/science.abo5672. This article has 41 citations and is from a highest quality peer-reviewed journal.

  12. (zanotti2022thehumansignal pages 57-60): Andrea Zanotti, João P. L. Coelho, Dinah Kaylani, Gurdeep Singh, Marina Tauber, Manuel Hitzenberger, Dönem Avci, Martin Zacharias, Robert B. Russell, Marius K. Lemberg, and Matthias J. Feige. The human signal peptidase complex acts as a quality control enzyme for membrane proteins. Science, 378:996-1000, Dec 2022. URL: https://doi.org/10.1126/science.abo5672, doi:10.1126/science.abo5672. This article has 41 citations and is from a highest quality peer-reviewed journal.

  13. (zanotti2023characterisationofthe pages 57-60): Andrea Zanotti. Characterisation of the human signal peptidase complex as a quality control enzyme for membrane proteins. Text, Jan 2023. URL: https://doi.org/10.11588/heidok.00033417, doi:10.11588/heidok.00033417. This article has 0 citations and is from a peer-reviewed journal.

  14. (estoppey2017thenaturalproduct pages 4-5): David Estoppey, Chia Min Lee, Marco Janoschke, Boon Heng Lee, Kah Fei Wan, Hongping Dong, Philippe Mathys, Ireos Filipuzzi, Tim Schuhmann, Ralph Riedl, Thomas Aust, Olaf Galuba, Gregory McAllister, Carsten Russ, Martin Spiess, Tewis Bouwmeester, Ghislain M.C. Bonamy, and Dominic Hoepfner. The natural product cavinafungin selectively interferes with zika and dengue virus replication by inhibition of the host signal peptidase. Cell reports, 19 3:451-460, Apr 2017. URL: https://doi.org/10.1016/j.celrep.2017.03.071, doi:10.1016/j.celrep.2017.03.071. This article has 101 citations and is from a highest quality peer-reviewed journal.

  15. (cui2015competitiveinhibitionof pages 1-2): Jingqiu Cui, Wei Chen, Jinhong Sun, Huan Guo, Rachel Madley, Yi Xiong, Xingyi Pan, Hongliang Wang, Andrew W. Tai, Michael A. Weiss, Peter Arvan, and Ming Liu. Competitive inhibition of the endoplasmic reticulum signal peptidase by non-cleavable mutant preprotein cargos. Journal of Biological Chemistry, 290:28131-28140, Nov 2015. URL: https://doi.org/10.1074/jbc.m115.692350, doi:10.1074/jbc.m115.692350. This article has 33 citations and is from a domain leading peer-reviewed journal.

  16. (zanotti2023characterisationofthe pages 53-57): Andrea Zanotti. Characterisation of the human signal peptidase complex as a quality control enzyme for membrane proteins. Text, Jan 2023. URL: https://doi.org/10.11588/heidok.00033417, doi:10.11588/heidok.00033417. This article has 0 citations and is from a peer-reviewed journal.

Artifacts

Citations

  1. liaci2021structureofthe pages 3-4
  2. liaci2021structureofthe pages 1-3
  3. zanotti2022thehumansignal pages 57-60
  4. estoppey2017thenaturalproduct pages 4-5
  5. zanotti2022thehumansignal pages 26-30
  6. cui2015competitiveinhibitionof pages 1-2
  7. zanotti2022thehumansignal pages 1-8
  8. zanotti2022thehumansignal pages 53-57
  9. liaci2021structureofthe pages 7-8
  10. zanotti2023characterisationofthe pages 57-60
  11. zanotti2023characterisationofthe pages 53-57
  12. https://doi.org/10.1074/jbc.m115.692350
  13. https://doi.org/10.2139/ssrn.3778304
  14. https://doi.org/10.1126/science.abo5672
  15. https://doi.org/10.11588/heidok.00033417
  16. https://doi.org/10.1083/jcb.202211035
  17. https://doi.org/10.2139/ssrn.3778304,
  18. https://doi.org/10.1126/science.abo5672,
  19. https://doi.org/10.1083/jcb.202211035,
  20. https://doi.org/10.11588/heidok.00033417,
  21. https://doi.org/10.1016/j.celrep.2017.03.071,
  22. https://doi.org/10.1074/jbc.m115.692350,

📚 Additional Documentation

Notes

(SEC11C-notes.md)

SEC11C (Q9BY50, SPC21) review notes

Identity / overview

SEC11C is a single-pass type II ER membrane protein and one of the two catalytic serine-endopeptidase
subunits of the human signal peptidase complex (SPC). It is the proteolytic subunit of the SPC-C paralog
(with accessory subunits SPCS1, SPCS2, SPCS3) and cleaves N-terminal signal/leader peptides from secretory
and membrane pre-proteins as they are translocated into the ER lumen (EC 3.4.21.89). Peptidase family S26B;
Ser/His/Asp charge-relay catalytic triad (catalytic Ser-68). It is the paralog of SEC11A (SPC-A).

  • UniProt FUNCTION: "Catalytic component of the signal peptidase complex (SPC) which catalyzes the cleavage
    of N-terminal signal sequences from nascent proteins as they are translocated into the lumen of the
    endoplasmic reticulum"; specificity for h-regions shorter than 18-20 aa [file:human/SEC11C/SEC11C-uniprot.txt].
  • SUBUNIT: "Component of the signal peptidase complex paralog C (SPC-C) composed of a catalytic subunit
    SEC11C and three accessory subunits SPCS1, SPCS2 and SPCS3 ... Within the complex, interacts with SPCS2
    and SPCS3" [file:human/SEC11C/SEC11C-uniprot.txt].
  • SUBCELLULAR LOCATION: "Endoplasmic reticulum membrane ... Single-pass type II membrane protein"
    [file:human/SEC11C/SEC11C-uniprot.txt].
  • Catalytic triad ACT_SITE 68/108/134; MUTAGEN S68A "Loss of catalytic activity"; CTS helix essential
    [file:human/SEC11C/SEC11C-uniprot.txt].

Key functional evidence

  • Structure of the human SPC: PMID:34388369 (Liaci et al., Mol Cell 2021): "the human SPC exists in two
    functional paralogs with distinct proteolytic subunits"; "The active site is formed by a catalytic
    triad and abuts the ER membrane ... locally thins the bilayer" PMID:34388369. EXP/IDA support for the
    catalytic and complex-membership annotations of SEC11C (SPC-C).

Annotation review decisions

  • Core MF: serine-type endopeptidase activity (GO:0004252) / signal peptidase activity (GO:0009003);
    generic peptidase activity (GO:0008233) ACCEPTed as parent.
  • Core CC: signal peptidase complex (GO:0005787); ER membrane (GO:0005789); generic membrane (GO:0016020)
    KEEP_AS_NON_CORE.
  • Core BP: signal-peptide cleavage captured by protein processing (GO:0016485) / protein maturation
    (GO:0051604). GO:0006465 (signal peptide processing) is in UniProt DR but not in the GOA tsv, so
    core_functions uses GO:0016485 (present in GOA).
  • protein binding (GO:0005515) IPI rows: high-throughput captures (BioPlex PMID:28514442, HuRI
    PMID:32296183, BioPlex PMID:33961781, cell-map PMID:40205054) + intra-complex SPCS2/SPCS3 (PMID:34388369).
    KEEP_AS_NON_CORE.
  • No "response to virus" annotation for SEC11C (unlike SEC11A).

Falcon deep-research findings (incorporated 2026-06)

The Falcon report (Edison Scientific) for SEC11C is built almost entirely on literature already in
the review: Liaci 2021 SPC cryo-EM (PMID:34388369), the Zanotti/Feige SPC quality-control function
(PMID:36454823, Science 2022), Chung 2024 Spc2 yeast study (PMID:39565596), and cavinafungin
(PMID:28423309). All already incorporated.

  • NEW reference added: Cui et al. 2015, competitive inhibition of ER signal peptidase by
    non-cleavable preprotein cargos PMID:26446786. PubMed-verified (DOI 10.1074/jbc.M115.692350,
    J Biol Chem 2015). Note: the abstract names SEC11A (not SEC11C) as the bound catalytic subunit, so
    relevance to SEC11C is LOW (background for the conserved eukaryotic SPase catalytic mechanism and
    druggability). Not in GOA; no new GO annotation.
  • Falcon emphasises SEC11A/SEC11C paralog redundancy: SEC11A knockdown did not abolish noncanonical
    cleavage of Cx32, "consistent with compensation by SEC11C," and notes SEC11C can be hard to detect
    in some cell lines at baseline, suggesting a context-dependent/backup catalytic role
    [PMID:36454823 (Zanotti 2022) / the linked Zanotti 2023 thesis (heidok.00033417)]. This already
    matches the SEC11C review framing; no annotation change. The thesis (heidok.00033417) is a
    non-PMID secondary version of the Science paper and was not added as a separate reference.
  • Falcon notes both SEC11A- and SEC11C-containing SPC paralogs cleaved a pre-beta-lactamase model
    substrate with similar efficiency in vitro (Liaci 2021), supporting that SEC11C is a fully active
    catalytic paralog PMID:34388369. Consistent with existing GO:0009003/GO:0004252 ACCEPT decisions;
    no change.
  • Falcon's "ssrn.3778304" DOI for the Liaci structure is the preprint of PMID:34388369; not added.

Pn Notes

(SEC11C-pn-notes.md)

SEC11C PN Consistency Notes

  • Generated: 2026-06-18
  • Project: PROTEOSTASIS
  • Scope: PN consistency rereview against local AIGR review and available deep-research artifacts
  • UniProt: Q9BY50
  • AIGR review status: COMPLETE
  • Review batch: proteostasis-batch-2026-06-11
  • Batch change status: added

Source Files Checked

Deep Research Files

AIGR Review Snapshot

  • Description: SEC11C (SPC21, SEC11L3; EC 3.4.21.89) is a single-pass type II endoplasmic reticulum membrane protein and one of the two catalytic serine-endopeptidase subunits of the human signal peptidase complex (SPC). As the proteolytic subunit of the SPC-C paralog (with accessory subunits SPCS1, SPCS2 and SPCS3), SEC11C catalyzes cleavage of N-terminal signal (leader) peptides from secretory and membrane pre-proteins as they are translocated into the ER lumen. It belongs to peptidase family S26B and uses a Ser/His/Asp-type charge-relay catalytic system (Ser-68 nucleophile). Its active site abuts the ER membrane, where the complex locally thins the lipid bilayer, conferring selectivity for signal peptides whose hydrophobic h-region is shorter than ~18-20 residues. SEC11C is the paralog of the more broadly expressed SEC11A; the two catalytic subunits form distinct but functionally analogous SPC paralogs.
  • Existing/core annotation action counts: ACCEPT: 18; KEEP_AS_NON_CORE: 6

PN Consistency Summary

  • Consistency: Strong agreement. Deep research, review YAML, and PN all identify SEC11C as the catalytic serine-endopeptidase subunit of the SPC-C paralog (Ser-68 triad, EC 3.4.21.89), the paralog of SEC11A. PN's "ER signal peptidase" node correctly captures complex membership. No contradictions.
  • PN story / NEW pressure: Identical to SEC11A. PN asserts CC membership (GO:0005787) + broad transport (GO:0015031), both already in the review, which additionally carries the catalytic MF (GO:0009003/GO:0004252, EXP/IDA from PMID:34388369). PN under-specifies the catalytic MF rather than over-reaching. No NEW term. Conclude: already captured.
  • Evidence alignment: PN row carries no titles; review evidence (PMID:34388369 structure/triad; Reactome signalase reactions; PMID:36454823 QC redundancy with SEC11A; PMID:28423309 cavinafungin) and falcon deep research (liaci2021) converge on the catalytic identity. Note PMID:26446786 names SEC11A (not SEC11C) — review correctly downgraded its relevance to SEC11C to LOW (background only).
  • Verdict: CONSISTENT; PN captures CC membership but omits catalytic MF (already in review). No edit required.

Full Consistency Review

  • UniProt: Q9BY50 (SPC21) · batch: proteostasis-batch-2026-06-11 · review status: COMPLETE
  • PN placement: ER proteostasis|Protein transport|ER signal peptidase; PN-node mapping: group mapped, ok_for_propagation_to_go, GO:0005787 (signal peptidase complex); class GO:0015031 (protein transport).
  • Consistency: Strong agreement. Deep research, review YAML, and PN all identify SEC11C as the catalytic serine-endopeptidase subunit of the SPC-C paralog (Ser-68 triad, EC 3.4.21.89), the paralog of SEC11A. PN's "ER signal peptidase" node correctly captures complex membership. No contradictions.
  • PN story / NEW pressure: Identical to SEC11A. PN asserts CC membership (GO:0005787) + broad transport (GO:0015031), both already in the review, which additionally carries the catalytic MF (GO:0009003/GO:0004252, EXP/IDA from PMID:34388369). PN under-specifies the catalytic MF rather than over-reaching. No NEW term. Conclude: already captured.
  • Mapping strategy: Same as SEC11A: node maps the catalytic+accessory group to the CC GO:0005787, which is correct for membership but does not surface SEC11C's catalytic peptidase MF. Node need not change; a catalytic-vs-accessory distinction note belongs at the node. GO:0015031 acceptably broad; no over-reach.
  • Evidence alignment: PN row carries no titles; review evidence (PMID:34388369 structure/triad; Reactome signalase reactions; PMID:36454823 QC redundancy with SEC11A; PMID:28423309 cavinafungin) and falcon deep research (liaci2021) converge on the catalytic identity. Note PMID:26446786 names SEC11A (not SEC11C) — review correctly downgraded its relevance to SEC11C to LOW (background only).
  • Verdict: CONSISTENT; PN captures CC membership but omits catalytic MF (already in review). No edit required.
  • Recommended edits: [MAP] Same node-level note as SEC11A: flag that catalytic subunits SEC11A/SEC11C project signal peptidase MF (GO:0009003 / GO:0004252) distinct from the non-catalytic SPCS subunits.

PN Dossier Context

  • review_batch: proteostasis-batch-2026-06-11
  • review_yaml: genes/human/SEC11C/SEC11C-ai-review.yaml
  • PN workbook rows: 1

PN row 1: ER proteostasis | Protein transport | ER signal peptidase

  • UniProt: Q9BY50
  • In branches: ER
  • PN-node mapping records (path + ancestors):
    • [group] ER proteostasis|Protein transport|ER signal peptidase
      status=mapped scope=ok_for_propagation_to_go GO=[GO:0005787 signal peptidase complex]
      rationale: This PN group denotes ER signal peptidase complex components. The matching GO cellular-component term is the direct propagation target.
    • [class] ER proteostasis|Protein transport
      status=mapped scope=ok_for_propagation_to_go GO=[GO:0015031 protein transport]
      rationale: The PN ER Protein transport class groups ER-targeting and ER-insertion pathways. GO protein transport is the appropriate propagation target, while the source class remains ER-specific and broader than any single GO transport subtype.
    • [branch] ER proteostasis
      status=no_mapping scope= GO=[]
      rationale: Reviewed as a top-level PN branch. This is a systems/taxonomy umbrella, not a direct GO assertion; narrower child curations carry any propagating GO mappings.

Projected GO annotations (2)

  • GO:0015031 protein transport | scope=ok_for_propagation_to_go | goa_status=new_to_goa | from=ER proteostasis|Protein transport
  • GO:0005787 signal peptidase complex | scope=ok_for_propagation_to_go | goa_status=already_in_goa_exact | from=ER proteostasis|Protein transport|ER signal peptidase

Note

This file is generated from the current PROTEOSTASIS phase-1 dossier and local gene-review artifacts. Edit the source review, PN mapping, or dossier rather than this generated note when correcting the underlying curation.

📄 View Raw YAML

id: Q9BY50
gene_symbol: SEC11C
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: SEC11C (SPC21, SEC11L3; EC 3.4.21.89) is a single-pass type II endoplasmic reticulum membrane protein and one of the two catalytic serine-endopeptidase subunits of the human signal peptidase complex (SPC). As the proteolytic subunit of the SPC-C paralog (with accessory subunits SPCS1, SPCS2 and SPCS3), SEC11C catalyzes cleavage of N-terminal signal (leader) peptides from secretory and membrane pre-proteins as they are translocated into the ER lumen. It belongs to peptidase family S26B and uses a Ser/His/Asp-type charge-relay catalytic system (Ser-68 nucleophile). Its active site abuts the ER membrane, where the complex locally thins the lipid bilayer, conferring selectivity for signal peptides whose hydrophobic h-region is shorter than ~18-20 residues. SEC11C is the paralog of the more broadly expressed SEC11A; the two catalytic subunits form distinct but functionally analogous SPC paralogs.
existing_annotations:
- term:
    id: GO:0005787
    label: signal peptidase complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: part_of
  review:
    summary: SEC11C is the catalytic subunit of the signal peptidase complex (SPC-C paralog); membership in the SPC is its defining, conserved cellular component.
    action: ACCEPT
    reason: Core cellular component; SEC11C is the proteolytic subunit of the signal peptidase complex.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: Component of the signal peptidase complex paralog C (SPC-C)
- term:
    id: GO:0008233
    label: peptidase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: SEC11C is a peptidase; "peptidase activity" is a correct but generic parent of the specific serine-type endopeptidase/signal peptidase activity.
    action: ACCEPT
    reason: Correct general molecular function; the specific serine-type endopeptidase activity (GO:0004252) better captures SEC11C's catalytic role.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: Belongs to the peptidase S26B family
- term:
    id: GO:0004252
    label: serine-type endopeptidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: SEC11C is a serine-type endopeptidase that uses a Ser/His/Asp charge-relay catalytic triad to cleave signal peptides; this is its core molecular function.
    action: ACCEPT
    reason: Core molecular function; experimentally established serine-endopeptidase (signal peptidase) activity, supported by IDA/EXP and the catalytic triad.
    supported_by:
    - reference_id: PMID:34388369
      supporting_text: The active site is formed by a
- term:
    id: GO:0005787
    label: signal peptidase complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: part_of
  review:
    summary: ARBA electronic assignment of signal peptidase complex membership, redundant with the experimental IDA evidence.
    action: ACCEPT
    reason: Correct core cellular component; redundant with IDA/IBA evidence.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: Component of the signal peptidase complex paralog C (SPC-C)
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: Electronic assignment of ER membrane localization from the UniProt subcellular location, consistent with the single-pass type II ER membrane topology.
    action: ACCEPT
    reason: Correct core localization; SEC11C is a single-pass ER membrane protein.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum membrane'
- term:
    id: GO:0008233
    label: peptidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: InterPro-based electronic assignment of peptidase activity; a generic parent of the specific serine-type endopeptidase activity.
    action: ACCEPT
    reason: Correct general molecular function; GO:0004252 is the informative specific term.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: Belongs to the peptidase S26B family
- term:
    id: GO:0009003
    label: signal peptidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000003
  qualifier: enables
  review:
    summary: EC-based electronic assignment of signal peptidase activity (EC 3.4.21.89); this is SEC11C's specific catalytic function and is experimentally supported (EXP).
    action: ACCEPT
    reason: Core molecular function; SEC11C is the catalytic signal peptidase of the SPC-C complex (EC 3.4.21.89).
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: EC=3.4.21.89
- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: located_in
  review:
    summary: SEC11C is a membrane protein; "membrane" is a correct but generic parent of the specific ER membrane localization.
    action: KEEP_AS_NON_CORE
    reason: Correct but generic; ER membrane (GO:0005789) is the specific and informative localization.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: Single-pass type II membrane protein
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:28514442
  qualifier: enables
  review:
    summary: BioPlex (HCIP) high-throughput interactome capture; bare protein binding is uninformative for core function.
    action: KEEP_AS_NON_CORE
    reason: High-throughput interactome interaction; uninformative bare term not elevated to core per guidelines.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: 'Q9BY50; P61009: SPCS3'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  qualifier: enables
  review:
    summary: Binary interactome (HuRI) high-throughput capture; bare protein binding is uninformative.
    action: KEEP_AS_NON_CORE
    reason: High-throughput interactome interaction; uninformative bare term not elevated to core.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: 'Q9BY50; P61009: SPCS3'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33961781
  qualifier: enables
  review:
    summary: BioPlex proteome-scale interactome capture; bare protein binding is uninformative.
    action: KEEP_AS_NON_CORE
    reason: High-throughput interactome interaction; uninformative bare term not elevated to core.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: 'Q9BY50; P61009: SPCS3'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:34388369
  qualifier: enables
  review:
    summary: SEC11C interacts with the SPC accessory subunits SPCS2 and SPCS3 within the signal peptidase complex; the bare protein binding term is uninformative, but the SPC assembly is captured better by the signal peptidase complex part_of annotation.
    action: KEEP_AS_NON_CORE
    reason: Records genuine intra-complex interactions (SPCS2/SPCS3), but bare protein binding is uninformative; the functional content is captured by the signal peptidase complex CC.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: with SPCS2 and SPCS3
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:40205054
  qualifier: enables
  review:
    summary: Multimodal cell-map (proteomics/imaging) high-throughput capture; bare protein binding is uninformative for core function.
    action: KEEP_AS_NON_CORE
    reason: High-throughput interactome/cell-map interaction; uninformative bare term not elevated to core.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: 'Q9BY50; P61009: SPCS3'
- term:
    id: GO:0005787
    label: signal peptidase complex
  evidence_type: IPI
  original_reference_id: PMID:34388369
  qualifier: part_of
  review:
    summary: The cryo-EM structure identifies SEC11C within the assembled signal peptidase complex (SPC-C) with SPCS1/2/3; defining cellular component.
    action: ACCEPT
    reason: Core cellular component; SEC11C is the catalytic subunit of the structurally resolved SPC-C complex.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: Component of the signal peptidase complex paralog C (SPC-C)
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IDA
  original_reference_id: PMID:34388369
  qualifier: located_in
  review:
    summary: The SPC structure places SEC11C in the ER membrane, with the active site abutting the bilayer; direct experimental localization.
    action: ACCEPT
    reason: Core localization with direct experimental support; SEC11C acts at the ER membrane.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum membrane'
- term:
    id: GO:0016485
    label: protein processing
  evidence_type: IDA
  original_reference_id: PMID:34388369
  qualifier: involved_in
  review:
    summary: SEC11C processes pre-proteins by cleaving their signal peptides; "protein processing" is a correct but generic parent of the specific signal peptide processing.
    action: ACCEPT
    reason: Correct biological process; the specific signal peptide processing (GO:0006465) better captures SEC11C's role.
    supported_by:
    - reference_id: PMID:34388369
      supporting_text: it removes signal peptides (SPs) from a large
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: Sequence-similarity (ISS) transfer of ER membrane localization, consistent with the experimental IDA evidence.
    action: ACCEPT
    reason: Correct core localization; redundant with IDA/IEA ER membrane evidence.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum membrane'
- term:
    id: GO:0009003
    label: signal peptidase activity
  evidence_type: EXP
  original_reference_id: PMID:34388369
  qualifier: enables
  review:
    summary: Experimental demonstration (structure + catalytic-activity/mutagenesis of the catalytic triad including Ser-68) that SEC11C is a catalytic signal peptidase of the SPC. This is the core molecular function.
    action: ACCEPT
    reason: Core molecular function with direct experimental support; SEC11C is a catalytic signal peptidase subunit of the SPC.
    supported_by:
    - reference_id: PMID:34388369
      supporting_text: human SPC exists in two functional paralogs with distinct proteolytic
        subunits
- term:
    id: GO:0004252
    label: serine-type endopeptidase activity
  evidence_type: IDA
  original_reference_id: PMID:34388369
  qualifier: enables
  review:
    summary: Direct experimental demonstration of SEC11C serine-type endopeptidase (signal peptidase) activity via the resolved catalytic triad and catalytic-activity assays; core molecular function.
    action: ACCEPT
    reason: Core molecular function with direct experimental (IDA) support.
    supported_by:
    - reference_id: PMID:34388369
      supporting_text: The active site is formed by a
- term:
    id: GO:0005787
    label: signal peptidase complex
  evidence_type: IDA
  original_reference_id: PMID:34388369
  qualifier: part_of
  review:
    summary: Direct structural demonstration that SEC11C is the catalytic subunit within the assembled SPC-C; defining cellular component.
    action: ACCEPT
    reason: Core cellular component with direct experimental (IDA) support.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: Component of the signal peptidase complex paralog C (SPC-C)
- term:
    id: GO:0051604
    label: protein maturation
  evidence_type: IDA
  original_reference_id: PMID:34388369
  qualifier: involved_in
  review:
    summary: By cleaving signal peptides from pre-proteins, SEC11C contributes to maturation of secretory/membrane proteins; "protein maturation" is a correct but generic parent of the specific signal peptide processing.
    action: ACCEPT
    reason: Correct biological process; the specific signal peptide processing (GO:0006465) better captures SEC11C's role.
    supported_by:
    - reference_id: PMID:34388369
      supporting_text: it removes signal peptides (SPs) from a large
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-422051
  qualifier: located_in
  review:
    summary: Reactome curation of SEC11C ER membrane localization (preproghrelin signal peptide cleavage).
    action: ACCEPT
    reason: Correct core localization; redundant with experimental ER membrane evidence.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum membrane'
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9918795
  qualifier: located_in
  review:
    summary: Reactome curation of SEC11C ER membrane localization (flaviviral polyprotein signalase cleavage).
    action: ACCEPT
    reason: Correct core localization; redundant with experimental ER membrane evidence.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum membrane'
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9918871
  qualifier: located_in
  review:
    summary: Reactome curation of SEC11C ER membrane localization (NS4B signalase cleavage).
    action: ACCEPT
    reason: Correct core localization; redundant with experimental ER membrane evidence.
    supported_by:
    - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum membrane'
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000003
  title: Gene Ontology annotation based on Enzyme Commission mapping
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:28514442
  title: Architecture of the human interactome defines protein communities and disease
    networks.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: BioPlex (HCIP) interactome; source of a generic protein-binding IPI annotation.
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: High-throughput binary (HuRI/Y2H) interactome; source of a generic protein-binding IPI annotation.
- id: PMID:33961781
  title: Dual proteome-scale networks reveal cell-specific remodeling of the human
    interactome.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: BioPlex proteome-scale interactome; source of a generic protein-binding IPI annotation.
- id: PMID:34388369
  title: Structure of the human signal peptidase complex reveals the determinants
    for signal peptide cleavage.
  findings:
  - statement: The human signal peptidase complex exists in two functional paralogs with distinct proteolytic subunits (SEC11A and SEC11C); the active site is formed by a catalytic triad abutting the ER membrane, where a transmembrane window thins the bilayer to generate specificity for signal peptides based on the length of their hydrophobic segments.
    reference_section_type: ABSTRACT
  - statement: SEC11C is the catalytic subunit of SPC-C (with accessory subunits SPCS1, SPCS2, SPCS3); Ser-68 is the catalytic nucleophile and the C-terminal short (CTS) helix is essential for catalytic activity.
    reference_section_type: RESULTS
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Definitive structural/mechanistic study establishing SEC11C as a catalytic SPC paralog subunit, its catalytic triad, EC 3.4.21.89, and the membrane-thinning specificity mechanism.
- id: PMID:40205054
  title: Multimodal cell maps as a foundation for structural and functional genomics.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Multimodal cell-map (proteomics/imaging) study; source of a generic protein-binding IPI annotation.
- id: PMID:36454823
  title: The human signal peptidase complex acts as a quality control enzyme for membrane
    proteins.
  findings:
  - statement: Beyond canonical N-terminal signal peptide removal, the human SPC (catalytic
      core SEC11A/C with SPCS3) cleaves misfolded or unassembled membrane proteins
      at otherwise hidden "cryptic" cleavage sites abundant in the human membrane proteome;
      this post-translocational cleavage synergizes with ER-associated degradation
      (ERAD) to maintain membrane protein homeostasis. SEC11A knockdown did not abolish
      a noncanonical cleavage event, consistent with compensation by SEC11C.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: PubMed-verified (DOI 10.1126/science.abo5672, Science 2022). Establishes
      a membrane-protein quality-control function of the SPC catalytic core (SEC11A/C)
      and implicates SEC11C as a redundant/backup catalytic subunit when SEC11A is
      limiting. Not in GOA; informs BP context but no new SEC11C-specific GO annotation
      added.
- id: PMID:28423309
  title: The Natural Product Cavinafungin Selectively Interferes with Zika and Dengue
    Virus Replication by Inhibition of the Host Signal Peptidase.
  findings:
  - statement: Genome-wide CRISPR/Cas9 chemogenomic profiling in human cells and resistance
      selection in yeast identified the catalytic subunit of the signal peptidase
      (SEC11; human SEC11A and SEC11C) as the conserved efficacy target of cavinafungin,
      which rapidly blocks signal-sequence cleavage of host and viral proteins.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: PubMed-verified (DOI 10.1016/j.celrep.2017.03.071, Cell Rep 2017).
      Identifies human SEC11A/SEC11C as the conserved drug target; supports SEC11C's
      essential signal peptidase activity and chemical-biology/antiviral relevance.
- id: PMID:39565596
  title: Spc2 modulates substrate- and cleavage site-selection in the yeast signal
    peptidase complex.
  findings:
  - statement: In yeast, the noncatalytic SPC subunit Spc2 (ortholog of human SPCS2)
      modulates SPC discrimination between substrates and cleavage-site selection;
      molecular dynamics indicates Spc2 contributes to the membrane thinning at the
      center of the SPC that underlies substrate recognition, informing the conserved
      mechanism by which accessory subunits support the SEC11 catalytic subunit.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: PubMed-verified (DOI 10.1083/jcb.202211035, J Cell Biol 2024). Yeast
      study; mechanistically relevant to human SEC11C by clarifying how noncatalytic
      subunits shape substrate/cleavage-site selection of the SEC11 protease.
- id: PMID:26446786
  title: Competitive Inhibition of the Endoplasmic Reticulum Signal Peptidase by Non-cleavable
    Mutant Preprotein Cargos.
  findings:
  - statement: A non-cleavable variant preprotein (proline introduced immediately after
      the signal-peptide cleavage site) is translocated across the ER membrane where
      it binds the catalytic SPase subunit and inhibits signal peptidase activity in
      a dose-dependent manner; this work directly implicates SEC11A as the catalytic
      subunit and establishes eukaryotic SPase as a tractable antiviral target, informing
      the shared catalytic mechanism of the SEC11A/SEC11C signal peptidase paralogs.
    reference_section_type: ABSTRACT
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: PubMed-verified (PMID:26446786, DOI 10.1074/jbc.M115.692350, J Biol
      Chem 2015). Abstract names SEC11A (not SEC11C) as the bound catalytic subunit;
      relevant to SEC11C only as background for the conserved eukaryotic SPase catalytic
      mechanism and druggability. Not in GOA; no new core GO annotation added.
- id: Reactome:R-HSA-422051
  title: Cleavage of the signal peptide of Preproghrelin
  findings: []
- id: Reactome:R-HSA-9918795
  title: Signalase cleaves prM-E-NS1-NS2A
  findings: []
- id: Reactome:R-HSA-9918871
  title: Signalase cleaves prepro-NS4B
  findings: []
- id: file:human/SEC11C/SEC11C-uniprot.txt
  title: UniProt entry Q9BY50 (SC11C_HUMAN), Signal peptidase complex catalytic subunit
    SEC11C
  findings:
  - statement: SEC11C is the catalytic subunit of the signal peptidase complex paralog C (SPC-C) with SPCS1/2/3; cleaves N-terminal signal peptides (EC 3.4.21.89) from nascent proteins translocated into the ER lumen; single-pass type II ER membrane protein; peptidase S26B family; catalytic triad (Ser-68), selectivity for h-regions shorter than 18-20 residues via membrane thinning.
    reference_section_type: OTHER
core_functions:
- description: Catalytic serine-endopeptidase subunit of the ER signal peptidase complex (SPC-C paralog) that cleaves N-terminal signal peptides from secretory and membrane pre-proteins as they are translocated into the ER lumen, using a Ser/His/Asp catalytic triad.
  molecular_function:
    id: GO:0004252
    label: serine-type endopeptidase activity
  in_complex:
    id: GO:0005787
    label: signal peptidase complex
  supported_by:
  - reference_id: file:human/SEC11C/SEC11C-uniprot.txt
    supporting_text: catalyzes the cleavage of N-terminal signal sequences
  - reference_id: PMID:34388369
    supporting_text: The active site is formed by a
  directly_involved_in:
  - id: GO:0016485
    label: protein processing
proposed_new_terms: []
suggested_questions:
- question: What distinguishes the substrate specificity of the SEC11C (SPC-C) versus SEC11A (SPC-A) paralogous signal peptidase complexes, and do they serve distinct subsets of the secretory proteome or distinct tissues?
- question: How does the SPC's local thinning of the ER membrane mechanistically couple signal-peptide h-region length to catalytic engagement by SEC11C?
suggested_experiments:
- description: Reconstitute purified SPC-C (SEC11C + SPCS1/2/3) and assay cleavage of a panel of signal peptides varying in h-region length to quantify SEC11C's length-dependent specificity, comparing wild-type Ser-68 to the catalytic-dead S68A mutant.
- description: Acute degron depletion of SEC11C versus SEC11A followed by N-terminomics (e.g. TAILS) to define the paralog-specific repertoire of cleaved signal-peptide substrates in human cells.