CNPY3 (Protein canopy homolog 3; also known as PRAT4A, Protein Associated with TLR4) is an endoplasmic reticulum (ER)-resident, glycosylated protein of the canopy family. It has a cleaved N-terminal signal peptide and a single saposin-like / MD-2-related lipid-recognition (ML) domain (a Saposin B-type fold stabilized by three intramolecular disulfide bonds). CNPY3 functions as a Toll-like receptor (TLR)-specific co-chaperone that works together with the ER HSP90 paralog HSP90B1 (gp96 / GRP94 / endoplasmin). The CNPY3-HSP90B1 module mediates the folding and ER-to-surface/endosome trafficking of multiple TLRs, including the cell-surface receptors TLR1, TLR2, TLR4 and TLR5 and the endosomal nucleic-acid-sensing receptors TLR7 and TLR9, but not TLR3, which is CNPY3-independent. CNPY3 is therefore required for TLR exit from the ER and for innate immune signaling downstream of these receptors. The interaction between CNPY3 and HSP90B1 is disrupted by ATP, consistent with a HSP90-co-chaperone client-handoff cycle. Biallelic loss-of-function variants in CNPY3 cause autosomal recessive developmental and epileptic encephalopathy 60 (DEE60).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005102
signaling receptor binding
|
IBA
GO_REF:0000033 |
KEEP AS NON CORE |
Summary: Phylogenetic (IBA) annotation that CNPY3 enables signaling receptor binding. CNPY3 does physically engage the ectodomains of multiple TLRs in the ER as part of its folding/trafficking chaperone activity, so binding to these signaling receptors is supported. However, this term captures the client-engagement aspect but not the core chaperone/co-chaperone activity, and it does not distinguish CNPY3 from a true signaling effector.
Reason: CNPY3 binds TLR clients (TLR1/2/4/9) in the ER, so signaling receptor binding is defensible, but it is a downstream consequence of the chaperone function rather than the core molecular function. The more informative MF terms are unfolded protein binding and Hsp90 protein binding. Keep as non-core.
Supporting Evidence:
file:human/CNPY3/CNPY3-uniprot.txt
Interacts with HSP90B1; this interaction is disrupted in the presence of ATP. Interacts with TLR1, TLR2, TLR4 and TLR9. Strongest interaction with TLR4.
|
|
GO:0005783
endoplasmic reticulum
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: IEA annotation mapping the UniProt subcellular location (Endoplasmic reticulum) to GO. CNPY3 is an ER-resident protein with a signal peptide and an ER-luminal co-chaperone function.
Reason: ER localization is well established and central to CNPY3 function as an ER co-chaperone. The more specific term endoplasmic reticulum lumen (annotated separately) is also correct.
Supporting Evidence:
file:human/CNPY3/CNPY3-uniprot.txt
SUBCELLULAR LOCATION: Endoplasmic reticulum.
|
|
GO:0005515
protein binding
|
IPI
PMID:28514442 Architecture of the human interactome defines protein commun... |
MARK AS OVER ANNOTATED |
Summary: Bare "protein binding" annotation from a large-scale affinity purification-mass spectrometry interactome screen (BioPlex). The WITH/FROM partner (SLITRK4) is not a functionally relevant CNPY3 client.
Reason: Per curation guidelines, bare protein binding is uninformative and does not describe the molecular function of CNPY3. This interaction derives from a high-throughput proteomics dataset with no functional follow-up and an implausible partner; it should not be treated as core.
Supporting Evidence:
PMID:28514442
BioPlex 2.0 ... uses robust affinity purification-mass spectrometry methodology to elucidate protein interaction networks ... With more than 56,000 candidate interactions.
|
|
GO:0005515
protein binding
|
IPI
PMID:32296183 A reference map of the human binary protein interactome. |
MARK AS OVER ANNOTATED |
Summary: Bare "protein binding" annotation from the HuRI binary (yeast two-hybrid) interactome map. Partners (CLDN5, KCNJ6, FAM209A, GOLM1) are not functionally relevant CNPY3 clients.
Reason: Uninformative bare protein binding from a systematic all-by-all binary interactome screen, without functional characterization. Avoid bare protein binding per curation guidelines.
Supporting Evidence:
PMID:32296183
Here we present a human 'all-by-all' reference interactome map of human binary protein interactions, or 'HuRI'. With approximately 53,000 protein-protein interactions.
|
|
GO:0005515
protein binding
|
IPI
PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... |
MARK AS OVER ANNOTATED |
Summary: Bare "protein binding" annotation from a neurodegenerative-disease interactome mapping study. Partners (DMWD, WFS1, GRN, SPRED1, ATN1, KLK6, RNF11) are not functionally relevant CNPY3 clients.
Reason: Uninformative bare protein binding from a high-throughput interactome screen, without functional follow-up. Avoid bare protein binding per curation guidelines.
Supporting Evidence:
PMID:32814053
Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
|
|
GO:0005515
protein binding
|
IPI
PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... |
MARK AS OVER ANNOTATED |
Summary: Bare "protein binding" annotation from BioPlex 3.0 (cell-specific AP-MS interactome). The WITH/FROM partner (SLITRK4) is not a functionally relevant CNPY3 client.
Reason: Uninformative bare protein binding from a high-throughput proteomics dataset, without functional characterization. Avoid bare protein binding per curation guidelines.
Supporting Evidence:
PMID:33961781
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
|
|
GO:0005102
signaling receptor binding
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: IEA annotation transferred from the mouse ortholog (Cnpy3/Prat4A, Q9DAU1) via Ensembl Compara. Redundant with the IBA signaling receptor binding annotation; reflects CNPY3 engagement of TLR clients.
Reason: Same rationale as the IBA signaling receptor binding annotation: it captures TLR client engagement but not the core chaperone/co-chaperone molecular function. Keep as non-core.
Supporting Evidence:
file:human/CNPY3/CNPY3-uniprot.txt
Toll-like receptor (TLR)-specific co-chaperone for HSP90B1 ... Interacts with TLR1, TLR2, TLR4 and TLR9.
|
|
GO:0005788
endoplasmic reticulum lumen
|
TAS
Reactome:R-HSA-1678923 |
ACCEPT |
Summary: TAS annotation from Reactome (event "TLR folding by chaperones GP96 and CNPY3") placing CNPY3 in the ER lumen, where it acts as a co-chaperone with HSP90B1/gp96. Consistent with the signal-peptide-cleaved, ER-luminal topology of CNPY3.
Reason: ER lumen is the correct and most specific subcellular location for CNPY3 and is central to its co-chaperone function in TLR folding.
Supporting Evidence:
file:human/CNPY3/CNPY3-uniprot.txt
Reactome; R-HSA-1679131; Trafficking and processing of endosomal TLR.
|
|
GO:0005788
endoplasmic reticulum lumen
|
TAS
Reactome:R-HSA-1678944 |
ACCEPT |
Summary: TAS annotation from Reactome (event "Folded full-length TLR7/8/9 dissociates from the GP96:CNPY3 complex") placing CNPY3 in the ER lumen as part of the GP96:CNPY3 TLR-folding complex.
Reason: Duplicates the ER lumen localization, which is correct and central to CNPY3 function. The Reactome event directly describes the CNPY3:GP96 co-chaperone complex acting on TLR7/8/9.
Supporting Evidence:
file:human/CNPY3/CNPY3-uniprot.txt
Reactome; R-HSA-1679131; Trafficking and processing of endosomal TLR.
|
|
GO:0051082
unfolded protein binding
|
IC
file:human/CNPY3/CNPY3-uniprot.txt |
NEW |
Summary: Proposed new annotation capturing CNPY3's core chaperone activity: as a TLR-specific co-chaperone it binds unfolded/nascent TLR clients in the ER lumen to assist their folding.
Reason: The curated GOA does not represent CNPY3's chaperone molecular function. Unfolded protein binding is the most appropriate MF term for its client-binding activity.
Supporting Evidence:
file:human/CNPY3/CNPY3-uniprot.txt
Toll-like receptor (TLR)-specific co-chaperone for HSP90B1. Required for proper TLR folding, except that of TLR3.
|
|
GO:0051879
Hsp90 protein binding
|
IC
file:human/CNPY3/CNPY3-uniprot.txt |
NEW |
Summary: Proposed new annotation: CNPY3 binds the ER HSP90 paralog HSP90B1/gp96 directly as a co-chaperone; the interaction is ATP-sensitive.
Reason: Hsp90 protein binding is the most specific MF term for the well-documented CNPY3-HSP90B1 co-chaperone interaction, which is missing from GOA.
Supporting Evidence:
file:human/CNPY3/CNPY3-uniprot.txt
Interacts with HSP90B1; this interaction is disrupted in the presence of ATP.
|
|
GO:0034975
protein folding in endoplasmic reticulum
|
IC
file:human/CNPY3/CNPY3-uniprot.txt |
NEW |
Summary: Proposed new annotation for the biological process in which CNPY3 acts: assisting folding of TLRs in the ER lumen.
Reason: The process by which CNPY3 functions (TLR folding in the ER) is not annotated. GO:0034975 captures this directly.
Supporting Evidence:
file:human/CNPY3/CNPY3-uniprot.txt
Required for proper TLR folding ... and hence controls TLR exit from the endoplasmic reticulum.
|
|
GO:0045087
innate immune response
|
IC
file:human/CNPY3/CNPY3-uniprot.txt |
NEW |
Summary: Proposed new annotation: by enabling TLR folding and ER exit, CNPY3 is required for innate immune signaling. Supported by the UniProt Immunity/Innate immunity keywords and the GO:0045087 InterPro/keyword annotation in UniProt.
Reason: CNPY3 is required for innate immune responses via its role in TLR maturation; this BP is supported but not present in the curated GOA block.
Supporting Evidence:
file:human/CNPY3/CNPY3-uniprot.txt
Consequently, required for both innate and adaptive immune responses.
|
|
GO:0034123
positive regulation of toll-like receptor signaling pathway
|
IC
file:human/CNPY3/CNPY3-uniprot.txt |
NEW |
Summary: Proposed annotation not present in the current GOA for CNPY3.
Reason: By enabling TLR folding and ER exit, CNPY3 is required for TLR signaling; GO:0034123 captures its positive-regulatory role in this innate immune pathway.
|
Q: Does human CNPY3 directly bind the same TLR set (TLR1/2/4/5/7/9 but not TLR3) as established for mouse PRAT4A, and which TLR ectodomain regions are engaged by the saposin-like/ML domain?
Q: Is CNPY3 a general ER co-chaperone with additional non-TLR clients, or is its client repertoire restricted to TLRs?
Q: How does the DEE60-associated pathology relate to CNPY3 chaperone function - is it driven by impaired TLR trafficking/innate immunity, or by a separate neuronal client?
Experiment: Co-immunoprecipitation and proximity-labeling (e.g. BioID/APEX) of endogenous CNPY3 in human immune cells to define its direct clients and confirm ATP-sensitive HSP90B1 binding.
Experiment: CNPY3 knockout/knockdown in human cells followed by flow cytometry and surface/endosomal trafficking assays for TLR1/2/4/5/7/9 (and TLR3 as a negative control) to quantify TLR maturation and ER exit.
Experiment: Functional reconstitution of DEE60 patient missense variants (e.g. Gly125Arg) to test effects on CNPY3 stability, HSP90B1 binding, and TLR folding/trafficking.
UniProt: Q9BT09. Gene synonyms: CTG4A, ERDA5, PRAT4A (Protein Associated with TLR4), TNRC5. HGNC:11968. 278 aa precursor.
CNPY3 is an ER-resident, glycosylated protein with a signal peptide (1-30) and a single
Saposin B-type / MD-2-related lipid-recognition (ML) domain (47-271). It functions as a
Toll-like-receptor-specific co-chaperone for the ER HSP90 paralog HSP90B1 (gp96 / GRP94 / endoplasmin).
The mechanism was established originally in mouse (PRAT4A): gp96/HSP90B1 and CNPY3/PRAT4A
form a TLR-folding module required for cell-surface TLRs (TLR1/2/4/5/6) and endosomal nucleic-acid-sensing
TLRs (TLR7/9) to exit the ER; TLR3 is CNPY3-independent. The interaction between CNPY3 and gp96
is ATP-sensitive, consistent with a HSP90-cochaperone client-handoff cycle. [PMID:20865800 "Folding of
Toll-like receptors by the HSP90 paralogue gp96 requires a substrate-specific cochaperone"; cited in
file:human/CNPY3/CNPY3-uniprot.txt RN 8]
Biallelic loss-of-function variants in CNPY3 cause Developmental and epileptic encephalopathy 60
(DEE60, MIM:617929), autosomal recessive, with seizure onset in the first months of life.
A missense variant Gly125Arg is reported. [PMID:29394991 "Biallelic Variants in CNPY3, Encoding an
Endoplasmic Reticulum Chaperone, Cause Early-Onset Epileptic Encephalopathy"; file:human/CNPY3/CNPY3-uniprot.txt
DISEASE + RN 13]
Note: GO co-chaperone activity (GO:0003767) and chaperone cofactor-dependent refolding (GO:0051085) are
obsolete; GO:0061077 chaperone-mediated protein folding is obsolete. Use unfolded protein binding +
Hsp90 protein binding + protein folding in ER instead.
*-deep-research*.md file found in this gene directory.more_specific_than_existing_goa label is technically too weak: it is effectively new_to_goa. The review goes further and proposes a coherent NEW set (GO:0051082 unfolded protein binding, GO:0051879, GO:0034975 protein folding in ER, GO:0045087 innate immune response, GO:0034123 positive regulation of TLR signaling) — all defensible and well beyond the single PN term. ADD GO:0051879 confirmed.new_to_goa (not "more_specific"). Review's broader NEW terms are well supported.ER proteostasis|Chaperone|HSP90 system|HSP90 cochaperone|Folding of TLRs ; PN-node mapping: leaf [subtype] Folding of TLRs no_mapping; [type] HSP90 cochaperone → mapped GO:0051879 Hsp90 protein binding (more_specific_than_existing_goa); group/class/branch unmapped.more_specific_than_existing_goa label is technically too weak: it is effectively new_to_goa. The review goes further and proposes a coherent NEW set (GO:0051082 unfolded protein binding, GO:0051879, GO:0034975 protein folding in ER, GO:0045087 innate immune response, GO:0034123 positive regulation of TLR signaling) — all defensible and well beyond the single PN term. ADD GO:0051879 confirmed.[type] (cochaperone), leaving the "Folding of TLRs" leaf and HSP90-system containers unmapped — appropriate. Only refinement: the goa_status should be new_to_goa (no Hsp90-binding annotation exists in GOA), not more_specific_than_existing_goa.new_to_goa (not "more_specific"). Review's broader NEW terms are well supported.Recommended edits: [MAP] Correct goa_status for GO:0051879 on the CNPY3 row from more_specific_than_existing_goa to new_to_goa (no Hsp90-binding annotation exists in CNPY3 GOA). (Review already proposes GO:0051879 + the full chaperone/TLR NEW set; no YAML change needed.)
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.
id: Q9BT09
gene_symbol: CNPY3
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
CNPY3 (Protein canopy homolog 3; also known as PRAT4A, Protein Associated with
TLR4) is an endoplasmic reticulum (ER)-resident, glycosylated protein of the
canopy family. It has a cleaved N-terminal signal peptide and a single
saposin-like / MD-2-related lipid-recognition (ML) domain (a Saposin B-type
fold stabilized by three intramolecular disulfide bonds). CNPY3 functions as a
Toll-like receptor (TLR)-specific co-chaperone that works together with the ER
HSP90 paralog HSP90B1 (gp96 / GRP94 / endoplasmin). The CNPY3-HSP90B1 module
mediates the folding and ER-to-surface/endosome trafficking of multiple TLRs,
including the cell-surface receptors TLR1, TLR2, TLR4 and TLR5 and the
endosomal nucleic-acid-sensing receptors TLR7 and TLR9, but not TLR3, which is
CNPY3-independent. CNPY3 is therefore required for TLR exit from the ER and for
innate immune signaling downstream of these receptors. The interaction between
CNPY3 and HSP90B1 is disrupted by ATP, consistent with a HSP90-co-chaperone
client-handoff cycle. Biallelic loss-of-function variants in CNPY3 cause
autosomal recessive developmental and epileptic encephalopathy 60 (DEE60).
alternative_products:
- name: '1'
id: Q9BT09-1
- name: '2'
id: Q9BT09-2
sequence_note: VSP_030132, VSP_030133
existing_annotations:
- term:
id: GO:0005102
label: signaling receptor binding
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: >-
Phylogenetic (IBA) annotation that CNPY3 enables signaling receptor
binding. CNPY3 does physically engage the ectodomains of multiple TLRs in
the ER as part of its folding/trafficking chaperone activity, so binding to
these signaling receptors is supported. However, this term captures the
client-engagement aspect but not the core chaperone/co-chaperone activity,
and it does not distinguish CNPY3 from a true signaling effector.
action: KEEP_AS_NON_CORE
reason: >-
CNPY3 binds TLR clients (TLR1/2/4/9) in the ER, so signaling receptor
binding is defensible, but it is a downstream consequence of the chaperone
function rather than the core molecular function. The more informative MF
terms are unfolded protein binding and Hsp90 protein binding. Keep as
non-core.
supported_by:
- reference_id: file:human/CNPY3/CNPY3-uniprot.txt
supporting_text: >-
Interacts with HSP90B1; this interaction is disrupted in the presence of
ATP. Interacts with TLR1, TLR2, TLR4 and TLR9. Strongest interaction with
TLR4.
- term:
id: GO:0005783
label: endoplasmic reticulum
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: >-
IEA annotation mapping the UniProt subcellular location (Endoplasmic
reticulum) to GO. CNPY3 is an ER-resident protein with a signal peptide and
an ER-luminal co-chaperone function.
action: ACCEPT
reason: >-
ER localization is well established and central to CNPY3 function as an ER
co-chaperone. The more specific term endoplasmic reticulum lumen (annotated
separately) is also correct.
supported_by:
- reference_id: file:human/CNPY3/CNPY3-uniprot.txt
supporting_text: 'SUBCELLULAR LOCATION: Endoplasmic reticulum.'
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:28514442
qualifier: enables
review:
summary: >-
Bare "protein binding" annotation from a large-scale affinity
purification-mass spectrometry interactome screen (BioPlex). The WITH/FROM
partner (SLITRK4) is not a functionally relevant CNPY3 client.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Per curation guidelines, bare protein binding is uninformative and does not
describe the molecular function of CNPY3. This interaction derives from a
high-throughput proteomics dataset with no functional follow-up and an
implausible partner; it should not be treated as core.
supported_by:
- reference_id: PMID:28514442
supporting_text: >-
BioPlex 2.0 ... uses robust affinity purification-mass spectrometry
methodology to elucidate protein interaction networks ... With more than
56,000 candidate interactions.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:32296183
qualifier: enables
review:
summary: >-
Bare "protein binding" annotation from the HuRI binary (yeast two-hybrid)
interactome map. Partners (CLDN5, KCNJ6, FAM209A, GOLM1) are not
functionally relevant CNPY3 clients.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Uninformative bare protein binding from a systematic all-by-all binary
interactome screen, without functional characterization. Avoid bare protein
binding per curation guidelines.
supported_by:
- reference_id: PMID:32296183
supporting_text: >-
Here we present a human 'all-by-all' reference interactome map of human
binary protein interactions, or 'HuRI'. With approximately 53,000
protein-protein interactions.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:32814053
qualifier: enables
review:
summary: >-
Bare "protein binding" annotation from a neurodegenerative-disease
interactome mapping study. Partners (DMWD, WFS1, GRN, SPRED1, ATN1, KLK6,
RNF11) are not functionally relevant CNPY3 clients.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Uninformative bare protein binding from a high-throughput interactome
screen, without functional follow-up. Avoid bare protein binding per
curation guidelines.
supported_by:
- reference_id: PMID:32814053
supporting_text: >-
Interactome Mapping Provides a Network of Neurodegenerative Disease
Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:33961781
qualifier: enables
review:
summary: >-
Bare "protein binding" annotation from BioPlex 3.0 (cell-specific AP-MS
interactome). The WITH/FROM partner (SLITRK4) is not a functionally
relevant CNPY3 client.
action: MARK_AS_OVER_ANNOTATED
reason: >-
Uninformative bare protein binding from a high-throughput proteomics
dataset, without functional characterization. Avoid bare protein binding
per curation guidelines.
supported_by:
- reference_id: PMID:33961781
supporting_text: >-
Dual proteome-scale networks reveal cell-specific remodeling of the human
interactome.
- term:
id: GO:0005102
label: signaling receptor binding
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: enables
review:
summary: >-
IEA annotation transferred from the mouse ortholog (Cnpy3/Prat4A, Q9DAU1)
via Ensembl Compara. Redundant with the IBA signaling receptor binding
annotation; reflects CNPY3 engagement of TLR clients.
action: KEEP_AS_NON_CORE
reason: >-
Same rationale as the IBA signaling receptor binding annotation: it
captures TLR client engagement but not the core chaperone/co-chaperone
molecular function. Keep as non-core.
supported_by:
- reference_id: file:human/CNPY3/CNPY3-uniprot.txt
supporting_text: >-
Toll-like receptor (TLR)-specific co-chaperone for HSP90B1 ... Interacts
with TLR1, TLR2, TLR4 and TLR9.
- term:
id: GO:0005788
label: endoplasmic reticulum lumen
evidence_type: TAS
original_reference_id: Reactome:R-HSA-1678923
qualifier: located_in
review:
summary: >-
TAS annotation from Reactome (event "TLR folding by chaperones GP96 and
CNPY3") placing CNPY3 in the ER lumen, where it acts as a co-chaperone with
HSP90B1/gp96. Consistent with the signal-peptide-cleaved, ER-luminal
topology of CNPY3.
action: ACCEPT
reason: >-
ER lumen is the correct and most specific subcellular location for CNPY3
and is central to its co-chaperone function in TLR folding.
supported_by:
- reference_id: file:human/CNPY3/CNPY3-uniprot.txt
supporting_text: >-
Reactome; R-HSA-1679131; Trafficking and processing of endosomal TLR.
- term:
id: GO:0005788
label: endoplasmic reticulum lumen
evidence_type: TAS
original_reference_id: Reactome:R-HSA-1678944
qualifier: located_in
review:
summary: >-
TAS annotation from Reactome (event "Folded full-length TLR7/8/9
dissociates from the GP96:CNPY3 complex") placing CNPY3 in the ER lumen as
part of the GP96:CNPY3 TLR-folding complex.
action: ACCEPT
reason: >-
Duplicates the ER lumen localization, which is correct and central to CNPY3
function. The Reactome event directly describes the CNPY3:GP96 co-chaperone
complex acting on TLR7/8/9.
supported_by:
- reference_id: file:human/CNPY3/CNPY3-uniprot.txt
supporting_text: >-
Reactome; R-HSA-1679131; Trafficking and processing of endosomal TLR.
- term:
id: GO:0051082
label: unfolded protein binding
evidence_type: IC
original_reference_id: file:human/CNPY3/CNPY3-uniprot.txt
qualifier: enables
review:
summary: >-
Proposed new annotation capturing CNPY3's core chaperone activity: as a
TLR-specific co-chaperone it binds unfolded/nascent TLR clients in the ER
lumen to assist their folding.
action: NEW
reason: >-
The curated GOA does not represent CNPY3's chaperone molecular function.
Unfolded protein binding is the most appropriate MF term for its
client-binding activity.
supported_by:
- reference_id: file:human/CNPY3/CNPY3-uniprot.txt
supporting_text: >-
Toll-like receptor (TLR)-specific co-chaperone for HSP90B1. Required for
proper TLR folding, except that of TLR3.
- term:
id: GO:0051879
label: Hsp90 protein binding
evidence_type: IC
original_reference_id: file:human/CNPY3/CNPY3-uniprot.txt
qualifier: enables
review:
summary: >-
Proposed new annotation: CNPY3 binds the ER HSP90 paralog HSP90B1/gp96
directly as a co-chaperone; the interaction is ATP-sensitive.
action: NEW
reason: >-
Hsp90 protein binding is the most specific MF term for the well-documented
CNPY3-HSP90B1 co-chaperone interaction, which is missing from GOA.
supported_by:
- reference_id: file:human/CNPY3/CNPY3-uniprot.txt
supporting_text: >-
Interacts with HSP90B1; this interaction is disrupted in the presence of
ATP.
- term:
id: GO:0034975
label: protein folding in endoplasmic reticulum
evidence_type: IC
original_reference_id: file:human/CNPY3/CNPY3-uniprot.txt
qualifier: involved_in
review:
summary: >-
Proposed new annotation for the biological process in which CNPY3 acts:
assisting folding of TLRs in the ER lumen.
action: NEW
reason: >-
The process by which CNPY3 functions (TLR folding in the ER) is not
annotated. GO:0034975 captures this directly.
supported_by:
- reference_id: file:human/CNPY3/CNPY3-uniprot.txt
supporting_text: >-
Required for proper TLR folding ... and hence controls TLR exit from the
endoplasmic reticulum.
- term:
id: GO:0045087
label: innate immune response
evidence_type: IC
original_reference_id: file:human/CNPY3/CNPY3-uniprot.txt
qualifier: involved_in
review:
summary: >-
Proposed new annotation: by enabling TLR folding and ER exit, CNPY3 is
required for innate immune signaling. Supported by the UniProt
Immunity/Innate immunity keywords and the GO:0045087 InterPro/keyword
annotation in UniProt.
action: NEW
reason: >-
CNPY3 is required for innate immune responses via its role in TLR
maturation; this BP is supported but not present in the curated GOA block.
supported_by:
- reference_id: file:human/CNPY3/CNPY3-uniprot.txt
supporting_text: >-
Consequently, required for both innate and adaptive immune responses.
- term:
id: GO:0034123
label: positive regulation of toll-like receptor signaling pathway
evidence_type: IC
original_reference_id: file:human/CNPY3/CNPY3-uniprot.txt
qualifier: involved_in
review:
summary: Proposed annotation not present in the current GOA for CNPY3.
action: NEW
reason: >-
By enabling TLR folding and ER exit, CNPY3 is required for TLR signaling;
GO:0034123 captures its positive-regulatory role in this innate immune
pathway.
core_functions:
- description: >-
ER-resident, TLR-specific co-chaperone that binds the ER HSP90 paralog
HSP90B1 (gp96/GRP94) and, together with it, recognizes and assists the
folding of unfolded/nascent Toll-like receptors in the ER lumen.
molecular_function:
id: GO:0051082
label: unfolded protein binding
supported_by:
- reference_id: file:human/CNPY3/CNPY3-uniprot.txt
supporting_text: >-
Toll-like receptor (TLR)-specific co-chaperone for HSP90B1. Required for
proper TLR folding, except that of TLR3.
- description: >-
Binds the ER HSP90 chaperone HSP90B1 (gp96) directly as a substrate-specific
co-chaperone; the interaction is ATP-sensitive, consistent with a HSP90
client-handoff cycle.
molecular_function:
id: GO:0051879
label: Hsp90 protein binding
supported_by:
- reference_id: file:human/CNPY3/CNPY3-uniprot.txt
supporting_text: >-
Interacts with HSP90B1; this interaction is disrupted in the presence of
ATP.
- description: >-
Promotes folding of TLRs in the ER and controls their exit from the ER to the
cell surface (TLR1/2/4/5) or endosomes (TLR7/9), thereby enabling innate
immune signaling. TLR3 folding is CNPY3-independent.
directly_involved_in:
- id: GO:0034975
label: protein folding in endoplasmic reticulum
- id: GO:0045087
label: innate immune response
locations:
- id: GO:0005788
label: endoplasmic reticulum lumen
supported_by:
- reference_id: file:human/CNPY3/CNPY3-uniprot.txt
supporting_text: >-
Required for proper TLR folding ... and hence controls TLR exit from the
endoplasmic reticulum. Consequently, required for both innate and adaptive
immune responses.
proposed_new_terms: []
suggested_questions:
- question: Does human CNPY3 directly bind the same TLR set (TLR1/2/4/5/7/9 but not TLR3) as established for mouse PRAT4A, and which TLR ectodomain regions are engaged by the saposin-like/ML domain?
- question: Is CNPY3 a general ER co-chaperone with additional non-TLR clients, or is its client repertoire restricted to TLRs?
- question: How does the DEE60-associated pathology relate to CNPY3 chaperone function - is it driven by impaired TLR trafficking/innate immunity, or by a separate neuronal client?
suggested_experiments:
- description: Co-immunoprecipitation and proximity-labeling (e.g. BioID/APEX) of endogenous CNPY3 in human immune cells to define its direct clients and confirm ATP-sensitive HSP90B1 binding.
- description: CNPY3 knockout/knockdown in human cells followed by flow cytometry and surface/endosomal trafficking assays for TLR1/2/4/5/7/9 (and TLR3 as a negative control) to quantify TLR maturation and ER exit.
- description: Functional reconstitution of DEE60 patient missense variants (e.g. Gly125Arg) to test effects on CNPY3 stability, HSP90B1 binding, and TLR folding/trafficking.
references:
- 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:0000107
title: Automatic transfer of experimentally verified manual GO annotation data to
orthologs using Ensembl Compara
findings: []
- id: PMID:28514442
title: Architecture of the human interactome defines protein communities and disease
networks.
findings:
- statement: >-
Large-scale AP-MS interactome (BioPlex 2.0); reports a CNPY3 interaction
with SLITRK4 as an uncharacterized high-throughput hit, not a functionally
validated client.
reference_section_type: ABSTRACT
- id: PMID:32296183
title: A reference map of the human binary protein interactome.
findings:
- statement: >-
HuRI binary (Y2H) interactome map; CNPY3 interactions reported are
systematic screen hits without functional characterization.
reference_section_type: ABSTRACT
- id: PMID:32814053
title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins
and Uncovers Widespread Protein Aggregation in Affected Brains.
findings:
- statement: >-
Neurodegenerative-disease interactome mapping; CNPY3 interactions are
high-throughput screen hits, not functionally relevant chaperone clients.
reference_section_type: TITLE
- id: PMID:33961781
title: Dual proteome-scale networks reveal cell-specific remodeling of the human
interactome.
findings:
- statement: >-
BioPlex 3.0 cell-specific AP-MS interactome; CNPY3 interaction reported is
a high-throughput screen hit without functional follow-up.
reference_section_type: TITLE
- id: Reactome:R-HSA-1678923
title: TLR folding by chaperones GP96 and CNPY3
findings:
- statement: >-
CNPY3 acts in the ER lumen with GP96 (HSP90B1) to fold Toll-like receptors.
reference_section_type: OTHER
- id: Reactome:R-HSA-1678944
title: 'Folded full-length TLR7/8/9 dissociates from the GP96:CNPY3 complex '
findings:
- statement: >-
Folded full-length TLR7/8/9 dissociates from the GP96:CNPY3 co-chaperone
complex in the ER.
reference_section_type: OTHER
- id: file:human/CNPY3/CNPY3-uniprot.txt
title: UniProtKB entry Q9BT09 (CNPY3_HUMAN)
findings:
- statement: >-
Toll-like receptor (TLR)-specific co-chaperone for HSP90B1; required for
proper TLR folding (except TLR3) and controls TLR exit from the ER;
required for innate and adaptive immune responses. ER-localized; interacts
with HSP90B1 (ATP-disrupted) and with TLR1/2/4/9 (strongest with TLR4).
reference_section_type: OTHER