EMC1 (human, Q8N766) — review notes

Identity / architecture

• 993 aa precursor; cleaved signal peptide (1..22); large lumenal domain (23..962), single TM helix (963..983), short cytoplasmic tail (984..993) — i.e. a single-pass type I membrane protein [file:human/EMC1/EMC1-uniprot.txt "Single-pass type I membrane protein"].
• Large lumenal region is a GOLD-like / WD40-YVTN β-propeller (Gene3D 2.130.10.10; Pfam Beta-prop_EMC1_N + EMC1_C; InterPro IPR026895). N-glycosylated at N370/N818/N913; disulfides 227-237, 338-368. It is the largest EMC subunit and acts as a lumenal scaffold; it is non-catalytic.
• Belongs to the EMC1 family.

Function (EMC complex context)

• Component of the ER membrane protein complex (EMC) [file:human/EMC1/EMC1-uniprot.txt "Component of the ER membrane protein complex (EMC)."], a 9-10 subunit conserved ER insertase/chaperone PMID:32439656.
• The EMC enables energy-independent insertion of newly synthesized membrane proteins, preferring TMDs that are weakly hydrophobic or have destabilizing (charged/aromatic) features [file:human/EMC1/EMC1-uniprot.txt "enables the energy-independent insertion into endoplasmic"].
• EMC is a transmembrane-domain insertase: purified EMC in liposomes catalyzes insertion of tail-anchored substrates (e.g. squalene synthase) PMID:29242231.
• Cotranslational role in multipass biogenesis; engages clients after TMD clusters enriched for charged residues PMID:29809151.
• Sets topology: EMC inserts the first TMD of GPCRs co-translationally in N-exo orientation, cooperating with Sec61 PMID:30415835.
• Catalytic insertase vestibule is formed by EMC3 + EMC6, NOT EMC1 PMID:32439656. EMC1 contributes as a structural lumenal scaffold subunit (contributes_to / part_of qualifiers in GOA reflect this complex-level contribution).

Localization

• ER membrane (IDA) first established in the ERAD interaction-mapping study that identified EMC subunits [PMID:22119785; file:human/EMC1/EMC1-uniprot.txt "SUBCELLULAR LOCATION: Endoplasmic reticulum membrane"].

Disease

• Biallelic/monoallelic variants cause CAVIPMR (cerebellar atrophy, visual impairment, psychomotor retardation; MIM 616875), AR neurodegenerative disorder [file:human/EMC1/EMC1-uniprot.txt "Cerebellar atrophy, visual impairment, and psychomotor"]. Variants: T82M, G471R, G868R (PMID:26942288); A144T in retinitis pigmentosa (uncertain; PMID:23105016).

Protein-binding IPIs

• Three GO:0005515 IPI annotations all derive from SARS-CoV-2 interactome screens with viral partner P0DTC8 (ORF8) [file:human/EMC1/EMC1-uniprot.txt "Q8N766; P0DTC8: 8; Xeno"] — PMID:32353859, 33060197, 36217030. Bare protein binding, viral partner, not core EMC function → KEEP_AS_NON_CORE.

Review decisions summary

• Core: EMC complex membership (GO:0072546, part_of); ER membrane localization (GO:0005789); contribution to complex insertase activity (GO:0032977, contributes_to) and insertion processes (GO:0071816 TA, GO:0045050 stop-transfer) — ACCEPT.
• Generic parents (GO:0016020 membrane, GO:0032991 protein-containing complex, GO:0005783 ER) — correct but uninformative → KEEP_AS_NON_CORE.
• No REMOVE/MODIFY/UNDECIDED calls; all experimental/complex annotations verifiable and consistent.

Verification pass (2026-06-11) — verbatim supporting text confirmed

• EMC complex membership: uniprot "Component of the ER membrane protein complex (EMC)." [file:human/EMC1/EMC1-uniprot.txt].
• ER membrane localization: uniprot "SUBCELLULAR LOCATION: Endoplasmic reticulum membrane" (IDA from PMID:22119785, which is the ERAD interaction-mapping paper that identified EMC subunits) [file:human/EMC1/EMC1-uniprot.txt].
• TA insertion / insertase activity reconstituted: PMID:29242231 and PMID:29242231.
• Cotranslational multipass biogenesis & charged-residue clusters: PMID:29809151 and "immediately following \nclusters of TMDs enriched for charged residues".
• Topogenesis / N-exo first TMD of GPCRs, cooperates with Sec61: PMID:30415835 and "the co-translational \ninsertion of the first transmembrane domain (TMD)".
• Catalytic vestibule is EMC3+EMC6 (EMC1 is non-catalytic lumenal scaffold): PMID:32439656; EMC is "a conserved co- and \nposttranslational insertase at the ER." Note PMID:32439656 full_text_available: false (abstract only) but abstract suffices for cited claims.
• GO:0032977 (membrane insertase activity) carries contributes_to qualifier — correct framing for a scaffold subunit; the WHOLE complex has insertase activity. ACCEPT.
• GO:0032991 (protein-containing complex) IDA from PMID:28246125 (MGI; ZMPSTE24/influenza paper) — cached text has no EMC mention (abstract about ZMPSTE24 antiviral role); this is a generic complex co-purification annotation, generic parent of EMC complex → KEEP_AS_NON_CORE (do not REMOVE an IDA per guidelines).
• Three GO:0005515 protein binding IPI all target viral P0DTC8 (SARS-CoV-2 ORF8): uniprot "Q8N766; P0DTC8: 8; Xeno" → real virus-interactome captures, bare uninformative term → KEEP_AS_NON_CORE.

Falcon deep-research findings (incorporated 2026-06)

New recent (2023-2025) papers identified by Falcon deep research and verified against PubMed; added to the review references. EMC1-specific or EMC-complex-level findings not previously captured:

• EMC1 is the subunit that engages client transmembrane domains in the EMC's chaperone (holdase) mode, distinct from the EMC3/EMC6 insertase vestibule; EMC1 modulates client TMD orientation in the bilayer, and productive assembly reduces binding to the EMC chaperone site PMID:40753078. This strengthens EMC1's specific client-engagement role beyond a purely structural lumenal scaffold (added GO:0051082 unfolded protein binding as a chaperone-mode core function).
• First mammalian EMC-client structure: human EMC bound to a CaV1.2-CaVbeta3 channel assembly intermediate; defines EMC transmembrane (TM) and cytoplasmic (Cyto) docks, with EMC1 contributing to the TM dock that engages CaV1.2 VSD I (interface residues incl. Asp961, Arg981). EMC acts as a holdase; EMC and CaValpha2delta binding are mutually exclusive (ordered hand-off) [PMID:37196677 "EMC functions as a channel holdase that facilitates channel assembly"; "EMC and CaValpha2delta interactions with the channel are mutually exclusive"].
• Selectivity filter mechanism: positively charged residues at the EMC hydrophilic-vestibule entrance act as a charge-repulsion filter that rejects mitochondrial tail-anchored proteins and enforces the positive-inside rule; substrate captured by methionine-rich cytosolic loops PMID:37199759. Complex-level (not EMC1-specific) refinement of the insertion/topogenesis mechanism.
• Human EMC cryo-EM in apo and VDAC-bound states (3.47 A / 3.32 A) identifies a "gating plug" inside the hydrophilic vestibule and a conserved EMC-VDAC interaction at mitochondria-ER contact sites; the VDAC1-bound state appears insertion-incompetent, supporting EMC multifunctionality PMID:38517390. EMC1 is the large lumenal subunit in these structures.
• EMC1-specific human genetics expanded: 8 individuals from 5 Kuwaiti families homozygous for EMC1 c.245C>T (p.Thr82Met) with CAVIPMR (OMIM #616875); GDD 8/8, microcephaly 8/8, truncal hypotonia 8/8, visual impairment 7/7, failure to thrive 7/7; chorea newly added to the phenotypic spectrum PMID:38784058. Reinforces EMC1's essential neurodevelopmental role.
• Note (not added to YAML): Falcon also cited a 2023 review (Le et al., Cells, DOI:10.3390/cells12212579) noting EMC1 among genes linked to FEVR-like retinal phenotypes; this is review-level/contextual and the FEVR link for EMC1 is indirect, so it was kept in notes only.

GO:0051082 migration (2026-09-27)

The TMD-holding core function carries no molecular-function term. GO:0051082 described unfolded soluble proteins, not client transmembrane domains, and GO has no term for intramembrane TMD holding by an insertase subunit.