RPN2 (ribophorin II) is a non-catalytic subunit of the oligosaccharyltransferase (OST) complex, the endoplasmic-reticulum (ER) membrane enzyme that catalyzes the central, committed step of N-linked protein glycosylation. OST transfers a pre-assembled Glc3Man9GlcNAc2 oligosaccharide en bloc from the dolichol-pyrophosphate lipid carrier onto asparagine residues within Asn-X-Ser/Thr sequons of nascent secretory and membrane proteins. RPN2 is a multi-pass ER-membrane glycoprotein with a large lumenal domain and a C-terminal three-helix transmembrane region. It is one of the common non-catalytic core subunits (with RPN1/ribophorin I, DDOST/OST48, OST4, DAD1 and TMEM258) shared by the two human OST complexes: the co-translational, SEC61-associated OST-A complex (built around the catalytic subunit STT3A) and the post-translocational OST-B complex (built around STT3B). Within OST, RPN2 acts as a structural/accessory subunit that contributes to complex assembly and to full catalytic activity rather than performing catalysis itself. RPN2 is broadly expressed and, together with the other OST subunits, is essential for maturation of the many glycoproteins that transit the secretory pathway; loss-of-function is linked to a congenital disorder of glycosylation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008250 oligosaccharyltransferase complex | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) inference that RPN2 is part of the OST complex. This is the accurate, defining cellular-component annotation for RPN2 and is directly supported by structural and biochemical evidence, so it is accepted as a core annotation. More specific IDA annotations to OST-A (GO:0160226) and OST-B (GO:0160227) exist. Supporting Evidence: file:human/RPN2/RPN2-uniprot.txt Subunit of the oligosaccharyl transferase (OST) complex that |
| GO:0006487 protein N-linked glycosylation | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) inference that RPN2 is involved in protein N-linked glycosylation. This is the correct core biological process for an OST subunit and is well supported experimentally; accepted as a core annotation. Supporting Evidence: file:human/RPN2/RPN2-uniprot.txt consensus motif in nascent polypeptide chains, the first step in |
| GO:0005783 endoplasmic reticulum | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Electronic mapping from the UniProt Subcellular Location vocabulary. RPN2 is an ER protein; the term is correct but general. The more specific ER membrane term (GO:0005789) better captures the localization of this multi-pass membrane protein, so this generic ER annotation is kept as non-core. Supporting Evidence: file:human/RPN2/RPN2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic mapping from the UniProt Subcellular Location vocabulary to ER membrane. RPN2 is a multi-pass ER membrane protein, so this is the correct and specific cellular-component location; accepted as a core location annotation. Supporting Evidence: file:human/RPN2/RPN2-uniprot.txt pass membrane protein |
| GO:0008250 oligosaccharyltransferase complex | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO electronic annotation (InterPro:IPR008814, Swp1/ribophorin II) mapping to the OST complex. This is the gene's own correct core complex membership; even though redundant with the IBA/IDA annotations it is accepted rather than treated as an over-annotation. Supporting Evidence: file:human/RPN2/RPN2-uniprot.txt Subunit of the oligosaccharyl transferase (OST) complex that |
| GO:0016020 membrane | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO electronic annotation to the generic "membrane" term. RPN2 is indeed a membrane protein, but this term is far less informative than the ER membrane (GO:0005789) annotation. Kept as non-core. Supporting Evidence: file:human/RPN2/RPN2-uniprot.txt pass membrane protein |
| GO:0005515 protein binding | IPI PMID:32707033 Kinase Interaction Network Expands Functional and Disease Ro... | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" (GO:0005515) from a high-throughput kinase interaction network study (interaction with POMK / Q9H5K3). This term carries no information about RPN2's actual molecular function and represents an over-annotation; per policy an IPI protein-binding annotation is not removed but flagged. |
| GO:0005789 endoplasmic reticulum membrane | NAS PMID:31831667 Cryo-electron microscopy structures of human oligosaccharylt... | ACCEPT | Summary: ER membrane location asserted (NAS, ComplexPortal) on the basis of the cryo-EM structures of the human OST-A/OST-B complexes. RPN2 is a multi-pass ER membrane protein; the location is correct. Redundant with the IEA ER-membrane annotation; accepted as a core location. Supporting Evidence: file:human/RPN2/RPN2-uniprot.txt pass membrane protein |
| GO:0006487 protein N-linked glycosylation | IDA PMID:31831667 Cryo-electron microscopy structures of human oligosaccharylt... | ACCEPT | Summary: Experimental (IDA) annotation from the cryo-EM study of the human OST complexes, supporting RPN2's involvement in protein N-linked glycosylation as an OST subunit. This is the correct core biological process; accepted. Supporting Evidence: PMID:31831667 Oligosaccharyltransferase (OST) catalyzes the transfer of a high-mannose glycan file:human/RPN2/RPN2-uniprot.txt protein N-glycosylation (PubMed:31831667). N-glycosylation occurs |
| GO:0006487 protein N-linked glycosylation | NAS PMID:31831667 Cryo-electron microscopy structures of human oligosaccharylt... | KEEP AS NON CORE | Summary: NAS (ComplexPortal) duplicate of the involved_in protein N-linked glycosylation annotation from the same OST cryo-EM study. Correct core process but redundant with the IDA annotation from the same reference; kept as non-core. Supporting Evidence: PMID:31831667 Oligosaccharyltransferase (OST) catalyzes the transfer of a high-mannose glycan |
| GO:0008250 oligosaccharyltransferase complex | IPI PMID:31831667 Cryo-electron microscopy structures of human oligosaccharylt... | KEEP AS NON CORE | Summary: OST complex membership (IPI, ComplexPortal) from the cryo-EM structural study. Correct core complex membership; redundant with the IBA/IDA/IEA OST-complex annotations and superseded in specificity by the OST-A/OST-B IDA annotations. Kept as non-core. Supporting Evidence: PMID:31831667 cryo-electron microscopy structures of human oligosaccharyltransferase complexes |
| GO:0008250 oligosaccharyltransferase complex | NAS PMID:31831667 Cryo-electron microscopy structures of human oligosaccharylt... | KEEP AS NON CORE | Summary: NAS (ComplexPortal) duplicate of the OST complex membership from the same study. Correct but redundant with the IPI/IBA/IDA OST-complex annotations; kept as non-core. Supporting Evidence: PMID:31831667 cryo-electron microscopy structures of human oligosaccharyltransferase complexes |
| GO:0005783 endoplasmic reticulum | IDA GO_REF:0000052 | KEEP AS NON CORE | Summary: Experimental immunofluorescence (IDA, HPA) localization to the endoplasmic reticulum. Consistent with RPN2 being an ER protein. The term is general relative to the ER-membrane annotation; kept as non-core. Supporting Evidence: file:human/RPN2/RPN2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum |
| GO:0005783 endoplasmic reticulum | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Sequence-similarity (ISS) transfer of ER localization from the ortholog UniProtKB:F1PCT7. Correct but general and redundant with the experimental ER and specific ER-membrane annotations; kept as non-core. Supporting Evidence: file:human/RPN2/RPN2-uniprot.txt SUBCELLULAR LOCATION: Endoplasmic reticulum |
| GO:0160226 oligosaccharyltransferase complex A | IDA PMID:31831667 Cryo-electron microscopy structures of human oligosaccharylt... | ACCEPT | Summary: Experimental (IDA) annotation that RPN2 is a subunit of the STT3A-containing OST-A complex, from the cryo-EM structures of the human OST complexes. This is the specific, structurally-supported refinement of the generic OST complex term and is a core cellular-component annotation; accepted. Supporting Evidence: PMID:31831667 cryo-electron microscopy structures of human oligosaccharyltransferase complexes file:human/RPN2/RPN2-uniprot.txt different complex forms which contain common core subunits RPN1, RPN2, |
| GO:0160226 oligosaccharyltransferase complex A | IDA PMID:36697828 Visualization of translation and protein biogenesis at the E... | ACCEPT | Summary: Experimental (IDA) annotation of RPN2 in the OST-A complex from cryo-electron tomography of the ER translocon, which resolves the SEC61-OSTA-TRAP translocon as the most abundant ER-membrane translocon. Corroborates OST-A membership; accepted as core. Supporting Evidence: PMID:36697828 the most populated SEC61–OSTA–TRAP (69% of ER-bound particles) PMID:36697828 OSTA, which is responsible for co-translational N-glycosylation of substrates |
| GO:0160226 oligosaccharyltransferase complex A | IDA PMID:38670073 Positive selection CRISPR screens reveal a druggable pocket ... | ACCEPT | Summary: Experimental (IDA) annotation of RPN2 in the OST-A complex from the CRISPR/cryo-EM study of the STT3A-containing OST. RPN2 is a core subunit of OST-A; accepted as core. Supporting Evidence: PMID:38670073 oligosaccharyltransferase complex OST-A for N-glycosylation and cell-surface |
| GO:0160227 oligosaccharyltransferase complex B | IDA PMID:31831667 Cryo-electron microscopy structures of human oligosaccharylt... | ACCEPT | Summary: Experimental (IDA) annotation that RPN2 is a subunit of the STT3B-containing OST-B complex, from the cryo-EM structures of the human OST complexes. RPN2 is a common core subunit shared by both OST-A and OST-B; this is a core cellular-component annotation. Supporting Evidence: PMID:31831667 cryo-electron microscopy structures of human oligosaccharyltransferase complexes file:human/RPN2/RPN2-uniprot.txt different complex forms which contain common core subunits RPN1, RPN2, |
| GO:0005515 protein binding | IPI PMID:28169274 Armc5 deletion causes developmental defects and compromises ... | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" (GO:0005515) from the ARMC5 knockout / T-cell study (interaction with ARMC5 / Q96C12). This is an uninformative interaction annotation that does not describe RPN2's molecular function; per policy an IPI protein-binding annotation is not removed but flagged as over-annotated. |
| GO:0006487 protein N-linked glycosylation | IDA PMID:9642163 Interleukin-2 induces N-glycosylation in T-cells: characteri... | ACCEPT | Summary: Experimental (IDA) annotation from the biochemical purification of human lymphocyte OST, which identified ribophorin I, ribophorin II and a Wbp1 homologue as components of the N-glycosylation enzyme. Supports RPN2's involvement in protein N-linked glycosylation; accepted as core. Supporting Evidence: PMID:9642163 proteins as ribophorin I, ribophorin II (doublet), and a 50-kDa homologue of |
| GO:0008250 oligosaccharyltransferase complex | IDA PMID:9642163 Interleukin-2 induces N-glycosylation in T-cells: characteri... | ACCEPT | Summary: Experimental (IDA) OST-complex membership from the purification of human lymphocyte OST, which co-purified ribophorin II with the other OST subunits. Correct core complex membership; accepted. Supporting Evidence: PMID:9642163 proteins as ribophorin I, ribophorin II (doublet), and a 50-kDa homologue of |
| GO:0005515 protein binding | IPI PMID:29290612 Removal of RTF2 from Stalled Replisomes Promotes Maintenance... | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" (GO:0005515) capturing the interaction with DDI2 (Q5TDH0), reported in a replisome/genome-integrity study and recorded in UniProt as "Interacts with DDI2". This is an uninformative molecular-function annotation; per policy an IPI protein-binding annotation is kept but marked over-annotated. The interaction itself is real but does not define RPN2's function. Supporting Evidence: file:human/RPN2/RPN2-uniprot.txt both the Sec61 and TRAP complexes (By similarity). Interacts with DDI2 |
| GO:0005515 protein binding | IPI PMID:24965446 Host factors that interact with the pestivirus N-terminal pr... | MARK AS OVER ANNOTATED | Summary: Bare "protein binding" (GO:0005515) from a study of host factors interacting with the pestivirus Npro protease (with/from viral P19712). This is an uninformative, infection-context interaction annotation that does not describe RPN2's endogenous molecular function; per policy an IPI protein-binding annotation is kept but flagged as over-annotated. |
| GO:0016020 membrane | HDA PMID:19946888 Defining the membrane proteome of NK cells. | KEEP AS NON CORE | Summary: High-throughput (HDA) membrane-proteome identification of RPN2 in NK-like cells. Only supports the generic "membrane" localization, which is far less informative than the ER membrane annotation. Kept as non-core. |
| GO:0005789 endoplasmic reticulum membrane | TAS Reactome:R-HSA-446209 | KEEP AS NON CORE | Summary: TAS ER-membrane location from the Reactome reaction "Transfer of N-glycan to the protein", in which the OST complex (including RPN2) acts at the ER membrane. Correct core location; redundant with the IEA/NAS ER-membrane annotations. Kept as non-core. |
| GO:0005789 endoplasmic reticulum membrane | TAS Reactome:R-HSA-9694793 | KEEP AS NON CORE | Summary: TAS ER-membrane location from a Reactome N-glycosylation reaction record (viral spike protein glycosylation). Correct location but a substrate-specific pathway instance; redundant with the primary ER-membrane annotations. Kept as non-core. |
| GO:0005789 endoplasmic reticulum membrane | TAS Reactome:R-HSA-9816276 | KEEP AS NON CORE | Summary: TAS ER-membrane location from a Reactome N-glycosylation reaction record (CDH1 glycosylation). Correct location but a substrate-specific pathway instance; redundant with the primary ER-membrane annotations. Kept as non-core. |
| GO:0005789 endoplasmic reticulum membrane | TAS Reactome:R-HSA-9918962 | KEEP AS NON CORE | Summary: TAS ER-membrane location from a Reactome N-glycosylation reaction record (viral E protein glycosylation). Correct location but a substrate-specific pathway instance; redundant with the primary ER-membrane annotations. Kept as non-core. |
| GO:0005789 endoplasmic reticulum membrane | TAS Reactome:R-HSA-9918988 | KEEP AS NON CORE | Summary: TAS ER-membrane location from a Reactome N-glycosylation reaction record (pre-M protein glycosylation). Correct location but a substrate-specific pathway instance; redundant with the primary ER-membrane annotations. Kept as non-core. |
| GO:0005789 endoplasmic reticulum membrane | TAS Reactome:R-HSA-9919011 | KEEP AS NON CORE | Summary: TAS ER-membrane location from a Reactome N-glycosylation reaction record (pre-NS1 folding/glycosylation). Correct location but a substrate-specific pathway instance; redundant with the primary ER-membrane annotations. Kept as non-core. |
| GO:0005789 endoplasmic reticulum membrane | TAS Reactome:R-HSA-9931286 | KEEP AS NON CORE | Summary: TAS ER-membrane location from a Reactome N-glycosylation reaction record (CD274/PD-L1 glycosylation). Correct location but a substrate-specific pathway instance; redundant with the primary ER-membrane annotations. Kept as non-core. |
| GO:0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity | NAS PMID:15835887 Proteomic analysis of mammalian oligosaccharyltransferase re... | ACCEPT | Summary: NAS annotation, correctly using the contributes_to qualifier, that RPN2 contributes to the OST catalytic activity. RPN2 is a non-catalytic subunit (the catalytic site is in STT3A/STT3B), so it does not enable this activity independently; contributes_to is the right relation and this is the appropriate way to model the accessory subunit's link to the complex-level catalytic function. Accepted as a core (contributes_to) molecular function. Supporting Evidence: file:human/RPN2/RPN2-uniprot.txt required for a maximal enzyme activity. |
| GO:0036211 protein modification process | TAS PMID:10660554 Retention of subunits of the oligosaccharyltransferase compl... | KEEP AS NON CORE | Summary: TAS annotation to the very general "protein modification process". RPN2's actual role is the more specific protein N-linked glycosylation (GO:0006487), which is already annotated with experimental evidence. This term is not wrong but is uninformatively broad; kept as non-core. (The cited paper is actually about ER retention of OST subunits including RII.) Supporting Evidence: PMID:10660554 proteins, ribophorin I (RI), ribophorin II (RII), and OST48. Together with DAD1 |
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Download this section (compressed HTML)Q: Does RPN2 make a defined mechanistic contribution to OST catalysis or substrate selection - for example acceptor-sequon presentation or lipid-linked oligosaccharide handoff - or is its role purely structural, stabilizing the STT3A/STT3B core? A contributes_to GO:0004579 annotation is currently justified only at the complex level.
Suggested experts: Locher KP, Ramírez AS, Kelleher DJ, Gilmore R
Q: Do the OST-A and OST-B complexes differ in their requirement for RPN2, and is the reported CDG-associated RPN2 variant selectively deleterious to one of the two complexes?
Suggested experts: Locher KP, Contessa JN, Lampson BL
Q: Is RPN2's large lumenal domain a bona fide chaperone/substrate-recruitment module for nascent glycoproteins, which would justify a more specific molecular function term than structural molecule activity?
Suggested experts: Kreibich G, Gilmore R, Förster F
Experiment: Generate RPN2 knockout and degron-tagged HEK293 or HAP1 lines, then quantify OST-A (STT3A) and OST-B (STT3B) complex integrity by blue-native PAGE and interaction proteomics, and measure site-specific N-glycosylation occupancy across the glycoproteome by intact-glycopeptide mass spectrometry after PNGase F/Endo H in 18O water. Compare the occupancy signature with that of STT3A and STT3B single knockouts to test whether RPN2 loss phenocopies both.
Hypothesis: RPN2 is required for assembly and stability of both OST-A and OST-B, and its loss reduces N-glycosylation site occupancy globally rather than for a defined substrate class.
Type: knockout glycoproteomics and native complex analysis
Experiment: Perform site-specific photo-crosslinking (incorporating p-benzoyl-phenylalanine at lumenal-domain positions guided by the OST-A/OST-B cryo-EM structures) in ER microsomes translating defined glycoprotein substrates, and identify crosslinked nascent chains by mass spectrometry. Complement with cryo-EM of OST-A stalled on a ribosome-nascent-chain complex to look for RPN2-substrate density.
Hypothesis: The lumenal domain of RPN2 contacts nascent acceptor polypeptides and contributes to sequon presentation rather than acting only as a scaffold.
Type: site-specific photo-crosslinking and structural analysis
Experiment: Reconstitute patient-derived RPN2 variants in RPN2-null cells and assay OST complex assembly (blue-native PAGE, STT3A/STT3B steady-state levels), in vitro oligosaccharyltransferase activity on a synthetic acceptor peptide with purified complexes, and transferrin/ApoC-III isoform profiling as a clinical CDG readout.
Hypothesis: RPN2 loss-of-function variants cause a congenital disorder of glycosylation through destabilization of the OST core rather than through loss of an RPN2-specific catalytic contribution.
Type: variant complementation and in vitro OST activity assay
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