{"gene":"RPN2","run_date":"2026-06-10T07:46:27","timeline":{"discoveries":[{"year":2008,"finding":"RPN2 silencing reduced N-glycosylation of P-glycoprotein (MDR1) and decreased its membrane localization, thereby sensitizing docetaxel-resistant breast cancer cells (MCF7-ADR) to docetaxel-induced apoptosis.","method":"siRNA knockdown, glycosylation assay, membrane localization analysis, apoptosis assay in breast cancer cells and in vivo xenograft models","journal":"Nature medicine","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean siRNA KD with specific cellular phenotype (glycosylation reduction, membrane mislocalization, apoptosis), validated in vivo, replicated across multiple resistance models","pmids":["18724378"],"is_preprint":false},{"year":2014,"finding":"RPN2 mediates N-glycosylation of tetraspanin CD63; knockdown of RPN2 reduces CD63 glycosylation and delocalizes CD63, which in turn displaces MDR1 from the cell surface and reduces chemoresistance and invasion in breast cancer cells.","method":"siRNA knockdown of RPN2 and CD63, glycosylation assay, co-localization/membrane fractionation, Transwell invasion assay, drug resistance assay","journal":"Molecular cancer","confidence":"High","confidence_rationale":"Tier 2 / Strong — orthogonal knockdown experiments (RPN2 and CD63 separately), glycosylation assay, functional readouts (invasion, drug resistance), builds on prior validated mechanism","pmids":["24884960"],"is_preprint":false},{"year":2012,"finding":"Yeast Rpn2 (proteasome subunit) directly binds ubiquitin receptor Rpn13 at its C-terminus, and stabilizes the association of Rpn10 with the central solenoid portion of Rpn1, coordinating multiple ubiquitin-processing factors at the 19S regulatory particle.","method":"Biochemical binding assays (association/dissociation constants), Co-IP, affinity measurements in yeast proteasome system","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding assays with quantitative affinity measurements, multiple binding partners tested with orthogonal approaches","pmids":["22318722"],"is_preprint":false},{"year":2012,"finding":"The eleven PC repeats of Rpn2 form a closed toroidal structure with two concentric rings of α-helices encircling two axial α-helices; the C-terminal 20 residues of Rpn2 serve as the docking site for ubiquitin receptor Rpn13.","method":"X-ray crystallography / structural determination of Rpn2 PC domain; binding assays for Rpn13","journal":"Structure (London, England : 1993)","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional domain mapping, consistent with independent biochemical data from other labs","pmids":["22405010"],"is_preprint":false},{"year":2004,"finding":"The bipartite nuclear localization sequence (NLS) of yeast Rpn2 is required for nuclear import of proteasomal base complexes via the karyopherin αβ pathway; deletion of the Rpn2 NLS results in improper nuclear proteasome localization and impaired proteasome function.","method":"NLS deletion mutagenesis, karyopherin pathway analysis, nuclear localization assay, proteasome function assay in yeast","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — NLS deletion mutant with direct localization and functional readout, karyopherin dependence established by epistasis","pmids":["15210724"],"is_preprint":false},{"year":2017,"finding":"The C-terminal 14 residues of human RPN2 constitute the binding epitope for RPN13/ADRM1's N-terminal PRU domain; crystal structures of the RPN13 PRU domain in complex with RPN2 C-terminal peptides and ubiquitin were determined, and mutagenesis validated the binding interface. RPN2, ubiquitin, and UCH37 bind RPN13 with independent energetics.","method":"Crystal structure determination, surface plasmon resonance, fluorescence polarization, mutational analysis using human proteins","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures plus mutagenesis plus quantitative biophysical binding assays, multiple orthogonal methods in one study","pmids":["28442575"],"is_preprint":false},{"year":2017,"finding":"A proline-rich C-terminal extension of hRpn2 stretches across a narrow canyon of the ubiquitin-binding Pru domain of hRpn13, blocking an RA190-binding surface; hRpn13 binds preferentially to hRpn2 and proteasomes over the anticancer compound RA190. RA190 does not affect hRpn13–Uch37 interaction but directly binds and inactivates Uch37.","method":"Crystal/NMR structure of hRpn13–hRpn2 complex, biophysical binding assays (SPR, ITC), cell-based assays with hRpn13 deletion in HCT116 cells","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — structure of the complex with biophysical validation plus cell-based functional assays, multiple orthogonal methods","pmids":["28598414"],"is_preprint":false},{"year":2019,"finding":"Phosphorylation of RPN2 Tyr-950 (identified in Jurkat cells) enhances RPN2 binding to RPN13; a crystal structure of the RPN2(pTyr-950)–RPN13–ubiquitin complex at 1.76 Å resolution reveals specific interactions with positively charged RPN13 side chains that explain the increased affinity without conformational change.","method":"Crystal structure at 1.76 Å, mutagenesis, quantitative binding assays (SPR, fluorescence polarization), phospho-site identification in cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution crystal structure combined with mutagenesis and quantitative biophysical assays","pmids":["31064842"],"is_preprint":false},{"year":2002,"finding":"Sequence analysis and molecular modeling predict that the PC repeat-containing domains of Rpn1/S2 and Rpn2/S1 adopt an α-helical toroid architecture with a central pore, proposed to form an antechamber for unfolded substrates ahead of the ATPase ring.","method":"Computational sequence analysis, molecular modeling","journal":"The Journal of biological chemistry","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational/modeling study only, no experimental validation in this paper (though later confirmed by crystallography)","pmids":["12270919"],"is_preprint":false},{"year":2017,"finding":"RPN2 knockdown reduced glycosylation of EGFR, decreased EGFR cell-surface transport, and attenuated EGFR/ERK signaling, thereby inhibiting colorectal cancer cell proliferation in vitro and in vivo.","method":"siRNA knockdown, glycosylation assay, EGFR cell-surface transport assay, ERK signaling analysis, in vitro proliferation and in vivo xenograft","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA KD with glycosylation assay and signaling readout, single lab, two orthogonal approaches","pmids":["29069815"],"is_preprint":false},{"year":2007,"finding":"IEX-1 (immediate early gene-X-1) reduces expression of proteasome subunits S1/Rpn2 and S5a/Rpn10 at the transcriptional level (interference with S5a promoter activity), leading to decreased 26S proteasome assembly and activity in HEK-293 cells.","method":"Overexpression of IEX-1 in HEK-293 cells, quantitative RT-PCR, luciferase promoter assay, cycloheximide/actinomycin D chase, 26S proteasome activity assay","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple methods (RT-PCR, promoter assay, drug chase, activity assay) in single lab","pmids":["17107344"],"is_preprint":false},{"year":2019,"finding":"RPN2 promotes hepatocellular carcinoma cell invasion by activating NF-κB p65 to upregulate MMP-9, and phosphorylated RPN2 activates STAT3, which also upregulates MMP-9 and promotes invasion.","method":"RPN2 overexpression and knockdown, western blot for MMP-9/NF-κB/STAT3, immunofluorescence, invasion assays in HCC cells","journal":"Aging","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single set of methods, pathway placement based on western blot without rigorous epistasis","pmids":["31481647"],"is_preprint":false},{"year":2018,"finding":"RPN2 knockdown in colon carcinoma cells reduced cell viability, increased apoptosis (caspase-3 upregulation), arrested cell cycle at G0/G1 (cyclin D1 reduction), and inhibited migration/invasion by regulating E-cadherin, MMP-2, and TIMP-2; STAT3 and JAK2 phosphorylation were reduced by RPN2 siRNA.","method":"siRNA knockdown, flow cytometry, Transwell assay, western blot, RT-PCR in colon cancer cell lines","journal":"Oncology reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, multiple phenotypic readouts but pathway placement (JAK2/STAT3) based on correlation western blots without epistasis","pmids":["29749494"],"is_preprint":false},{"year":2020,"finding":"RPN2 overexpression suppresses radiosensitivity of glioma cells by activating STAT3 signaling, which upregulates MCL1; depletion of RPN2 in radiation-resistant GBM cells sensitizes them to radiation-induced apoptosis.","method":"RPN2 overexpression/knockdown, radiation resistance assay, western blot for STAT3/MCL1, apoptosis assay in GBM cell lines","journal":"Molecular medicine (Cambridge, Mass.)","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, functional readout present but pathway placement relies on western blot correlation without rigorous mechanistic dissection","pmids":["32404045"],"is_preprint":false},{"year":2022,"finding":"The lncRNA WEE2-AS1 promotes RPN2 protein stabilization by preventing CUL2-mediated ubiquitination of RPN2 at K322, thereby activating the PI3K-Akt signaling pathway in glioblastoma cells.","method":"Mass spectrometry, RNA pulldown, RIP assay, Co-IP, luciferase reporter, ubiquitination assay identifying K322 as the ubiquitination site, PI3K-Akt pathway analysis","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ubiquitination site identified by MS with functional Co-IP and pathway readout, single lab but multiple orthogonal methods","pmids":["36168628"],"is_preprint":false},{"year":2019,"finding":"RPN2 overexpression promotes osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) by inducing JAK1 ubiquitination and activating JAK1/STAT3 signaling, promoting nuclear translocation of STAT3; depletion of JAK1 partially rescues the differentiation defect caused by RPN2 silencing.","method":"RPN2 overexpression/knockdown, alkaline phosphatase activity, western blot for JAK1/STAT3 phosphorylation and nuclear translocation, epistasis with JAK1 depletion, hBMSC differentiation assay","journal":"FEBS open bio","confidence":"Low","confidence_rationale":"Tier 3 / Weak — epistasis experiment present but mechanistic link between RPN2 and JAK1 ubiquitination lacks rigorous biochemical validation","pmids":["31743606"],"is_preprint":false},{"year":2025,"finding":"Cryo-EM structures of the human 26S proteasome bound to K11/K48-branched ubiquitin chains reveal a novel K11-linked ubiquitin binding site at the groove formed by RPN2 and RPN10, in addition to the canonical K48-linkage binding site; RPN2 recognizes alternating K11-K48 linkages through a conserved motif similar to the K48-specific T1 binding site of RPN1.","method":"Cryo-EM structural determination of human 26S proteasome–branched ubiquitin chain complex","journal":"bioRxiv (preprint)","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-quality cryo-EM structures but preprint, not yet peer-reviewed; single study","pmids":["bio_10.1101_2025.01.13.632666"],"is_preprint":true},{"year":2025,"finding":"High-resolution cryo-EM structures of the human 26S proteasome bound to K48-tetraubiquitin and K11/K48-branched chains reveal that K11 branches engage a cleft formed between RPN2 and RPN10; structure-guided mutagenesis confirms these binding modes are essential for efficient substrate degradation and cell cycle progression.","method":"Cryo-EM, structure-guided mutagenesis, substrate degradation assay, cell cycle analysis","journal":"bioRxiv (preprint)","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — cryo-EM plus mutagenesis plus functional cellular assay, single preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.04.07.647569"],"is_preprint":true},{"year":2025,"finding":"Eleven cryo-EM structures of the human 26S proteasome complexed with ODC reveal that Rpn2's PC domain participates in a multivalent, sequential recognition process for ubiquitin-independent ODC degradation, following initial engagement of the Rpn10 vWA domain and Rpt4/5 coiled-coil.","method":"Cryo-EM (11 structures capturing degradation intermediates), structural analysis of proteasome–ODC complex","journal":"bioRxiv (preprint)","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — multiple cryo-EM structures but preprint, single study, not peer-reviewed","pmids":["bio_10.1101_2025.11.15.688597"],"is_preprint":true},{"year":2024,"finding":"Cryo-EM structure of TXNL1 bound to the 19S regulatory particle reveals direct interactions between TXNL1 and PSMD1/Rpn2 (as well as Rpn10 and Rpn11), establishing the structural basis for ubiquitin-independent degradation of TXNL1 upon oxidative stress.","method":"Cryo-EM structural determination of TXNL1–19S proteasome complex","journal":"bioRxiv (preprint)","confidence":"Low","confidence_rationale":"Tier 1 / Weak — cryo-EM structure but preprint and single study; RPN2 role inferred from structural contact, not individually validated","pmids":["bio_10.1101_2024.11.08.622741"],"is_preprint":true},{"year":2021,"finding":"RPN2 overexpression in T lymphocytes inhibited apoptosis and IL-4 expression and promoted proliferation and activation, establishing a functional role for RPN2 in T lymphocyte growth and activation.","method":"Lentivirus-mediated RPN2 overexpression in T lymphocytes, flow cytometry for apoptosis and proliferation, cytokine measurement (IL-4), activation assays","journal":"Gene","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, overexpression-only approach, no pathway dissection or mechanistic follow-up","pmids":["34740730"],"is_preprint":false},{"year":1991,"finding":"RPN2 (ribophorin II) was chromosomally mapped to human chromosome 20q12-q13.1 by in situ hybridization; the protein was described as a glycoprotein spanning the rough endoplasmic reticulum, proposed to play a role in translocation or maintenance of RER.","method":"In situ hybridization chromosomal mapping","journal":"Human genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — chromosomal mapping only; functional role is inferred/proposed rather than directly demonstrated","pmids":["2066112"],"is_preprint":false}],"current_model":"Human RPN2 is a core scaffolding subunit of the 19S regulatory particle of the 26S proteasome, whose closed toroidal PC-repeat domain directly recruits ubiquitin receptor RPN13/ADRM1 via its C-terminal residues (with affinity enhanced by phosphorylation of Tyr-950), participates in K11/K48-branched and ubiquitin-independent substrate recognition alongside RPN10, and is required for karyopherin αβ-mediated nuclear import of the base complex; independently, as an obligate subunit of the oligosaccharyltransferase (OST) complex in the ER, RPN2 mediates N-linked glycosylation of substrates including P-glycoprotein/MDR1, CD63, and EGFR, thereby regulating their membrane localization, stability, and downstream signaling, with loss of this glycosylation activity sensitizing cancer cells to chemotherapy."},"narrative":{"mechanistic_narrative":"RPN2 is a dual-function protein that operates both as a scaffolding subunit of the 26S proteasome 19S regulatory particle and as a subunit of the ER oligosaccharyltransferase machinery [PMID:22405010, PMID:18724378]. Within the 19S particle, its eleven PC repeats fold into a closed α-helical toroid, and the C-terminal residues serve as the docking site that directly recruits the ubiquitin receptor RPN13/ADRM1, with RPN2 also stabilizing the association of RPN10 with the RPN1 solenoid to coordinate ubiquitin-processing factors [PMID:22405010, PMID:22318722, PMID:28442575]. Phosphorylation of RPN2 Tyr-950 enhances the affinity of this RPN13 interaction through specific contacts with positively charged RPN13 residues, without conformational change [PMID:31064842]. RPN2 contributes to substrate recognition at the proteasome, forming a groove with RPN10 that engages K11/K48-branched ubiquitin chains and participating in ubiquitin-independent degradation of substrates such as ODC [PMID:bio_10.1101_2025.04.07.647569, PMID:bio_10.1101_2025.11.15.688597], and its bipartite NLS directs karyopherin αβ-mediated nuclear import of the proteasomal base [PMID:15210724]. Independently, RPN2 mediates N-linked glycosylation of membrane substrates including P-glycoprotein/MDR1, CD63, and EGFR, controlling their cell-surface localization, stability, and signaling; loss of this activity mislocalizes MDR1 and sensitizes chemoresistant cancer cells to therapy [PMID:18724378, PMID:24884960, PMID:29069815].","teleology":[{"year":1991,"claim":"Established RPN2/ribophorin II as a rough-ER glycoprotein and placed it on the genetic map, the starting point for its ER-associated functions.","evidence":"in situ hybridization chromosomal mapping to 20q12-q13.1","pmids":["2066112"],"confidence":"Low","gaps":["functional role inferred, not demonstrated","no link to OST activity established here","no proteasomal role identified"]},{"year":2002,"claim":"Predicted the architecture of the RPN1/RPN2 PC-repeat domains as α-helical toroids forming an antechamber, framing the structural hypothesis later tested.","evidence":"computational sequence analysis and molecular modeling","pmids":["12270919"],"confidence":"Low","gaps":["no experimental structure in this work","function of the proposed antechamber untested"]},{"year":2004,"claim":"Answered how proteasomal base complexes reach the nucleus by identifying an RPN2 NLS, showing RPN2 has a localization-determining role beyond scaffolding.","evidence":"NLS deletion mutagenesis and karyopherin pathway/localization assays in yeast","pmids":["15210724"],"confidence":"High","gaps":["human NLS function not directly tested","regulation of import not addressed"]},{"year":2007,"claim":"Showed RPN2 abundance is transcriptionally regulated, linking proteasome assembly to upstream signaling via IEX-1.","evidence":"IEX-1 overexpression in HEK-293 with RT-PCR, promoter luciferase, and proteasome activity assays","pmids":["17107344"],"confidence":"Medium","gaps":["direct promoter binding by IEX-1 not shown","physiological context unclear"]},{"year":2008,"claim":"Revealed a chemoresistance function: RPN2 glycosylates MDR1 to maintain its membrane localization, so silencing RPN2 resensitizes resistant tumors.","evidence":"siRNA knockdown with glycosylation, membrane localization, apoptosis assays, and xenografts in breast cancer","pmids":["18724378"],"confidence":"High","gaps":["direct enzymatic glycosyltransferase role versus OST-complex dependence not dissected","scope of glycosylated substrates not defined here"]},{"year":2012,"claim":"Defined RPN2's molecular role at the 19S particle by mapping direct RPN13 binding to its C-terminus and showing it stabilizes RPN10, organizing ubiquitin-processing factors.","evidence":"quantitative binding assays and Co-IP in yeast plus X-ray crystallography of the PC toroid","pmids":["22318722","22405010"],"confidence":"High","gaps":["human complex interface not yet resolved","functional consequence of RPN13 docking for degradation not measured"]},{"year":2014,"claim":"Extended the glycosylation mechanism to CD63, showing RPN2-dependent CD63 glycosylation indirectly controls MDR1 surface display, invasion, and drug resistance.","evidence":"orthogonal RPN2 and CD63 knockdowns with glycosylation, fractionation, invasion, and resistance assays","pmids":["24884960"],"confidence":"High","gaps":["mechanism connecting CD63 glycosylation to MDR1 retention unresolved","in vivo validation limited"]},{"year":2017,"claim":"Resolved the human RPN2–RPN13 interface at atomic resolution, defining the C-terminal epitope and showing RPN13 binds RPN2, ubiquitin, and UCH37 with independent energetics; also explained why proteasomes outcompete the RA190 inhibitor for RPN13.","evidence":"crystal/NMR structures with SPR, ITC, fluorescence polarization, and cell-based assays using human proteins","pmids":["28442575","28598414"],"confidence":"High","gaps":["dynamics of RPN13 recruitment in intact proteasome not captured","therapeutic exploitation untested in vivo here"]},{"year":2017,"claim":"Generalized the glycosylation/membrane-localization mechanism to EGFR, linking RPN2 to EGFR/ERK-driven proliferation in colorectal cancer.","evidence":"siRNA knockdown with glycosylation, surface transport, ERK signaling, and xenograft assays","pmids":["29069815"],"confidence":"Medium","gaps":["direct enzymatic role versus OST dependence not separated","single lab"]},{"year":2019,"claim":"Showed RPN2 phosphorylation tunes proteasome function by demonstrating that pTyr-950 increases RPN13 affinity through defined electrostatic contacts.","evidence":"1.76 Å crystal structure of the RPN2(pTyr-950)–RPN13–ubiquitin complex with mutagenesis and biophysical assays","pmids":["31064842"],"confidence":"High","gaps":["kinase responsible for Tyr-950 phosphorylation unidentified","physiological trigger and consequence for degradation unknown"]},{"year":2019,"claim":"Reported pro-tumorigenic and differentiation roles for RPN2 via STAT3-axis signaling in HCC and bone marrow stem cells.","evidence":"overexpression/knockdown with western blot, immunofluorescence, invasion, and differentiation assays","pmids":["31481647","31743606"],"confidence":"Low","gaps":["pathway placement rests on correlative western blots","direct biochemical link between RPN2 and JAK1/STAT3 not validated"]},{"year":2022,"claim":"Identified post-translational control of RPN2 itself: lncRNA WEE2-AS1 blocks CUL2-mediated ubiquitination at K322 to stabilize RPN2 and activate PI3K-Akt signaling.","evidence":"MS, RNA pulldown, RIP, Co-IP, ubiquitination assay mapping K322, and pathway analysis in glioblastoma","pmids":["36168628"],"confidence":"Medium","gaps":["mechanism by which stabilized RPN2 activates PI3K-Akt unclear","single lab"]},{"year":2025,"claim":"Defined the structural basis for branched-chain and ubiquitin-independent substrate recognition, showing RPN2 forms a groove with RPN10 that engages K11/K48-branched ubiquitin and participates in sequential ODC and TXNL1 capture.","evidence":"cryo-EM of human 26S proteasome with branched ubiquitin, ODC, and TXNL1, plus structure-guided mutagenesis and degradation/cell-cycle assays (preprints)","pmids":["bio_10.1101_2025.01.13.632666","bio_10.1101_2025.04.07.647569","bio_10.1101_2025.11.15.688597","bio_10.1101_2024.11.08.622741"],"confidence":"Medium","gaps":["findings are preprints not yet peer-reviewed","RPN2-specific contribution to ODC/TXNL1 degradation inferred from structure","in vivo relevance of branched-chain site untested"]},{"year":null,"claim":"It remains unresolved whether RPN2's proteasomal scaffolding role and its ER glycosylation role are mechanistically coupled, and which kinases and physiological signals govern RPN2 phosphorylation and stability to switch between these functions.","evidence":"no timeline study integrates the two functional contexts","pmids":[],"confidence":"Low","gaps":["no study bridges OST and proteasome roles","upstream regulatory kinases unidentified","tissue-specific functional balance unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,3,5]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,9]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,21]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,9]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[2,3,5]}],"complexes":["26S proteasome 19S regulatory particle","oligosaccharyltransferase (OST) complex"],"partners":["RPN13/ADRM1","RPN10","RPN1","TXNL1","CUL2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P04844","full_name":"Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2","aliases":["Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunit","RIBIIR","Ribophorin II","RPN-II","Ribophorin-2"],"length_aa":631,"mass_kda":69.3,"function":"Subunit of the oligosaccharyl transferase (OST) complex that catalyzes the initial transfer of a defined glycan (Glc(3)Man(9)GlcNAc(2) in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation (PubMed:31831667). N-glycosylation occurs cotranslationally and the complex associates with the Sec61 complex at the channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). All subunits are required for a maximal enzyme activity","subcellular_location":"Endoplasmic reticulum; Endoplasmic reticulum membrane","url":"https://www.uniprot.org/uniprotkb/P04844/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPN2","classification":"Common Essential","n_dependent_lines":1098,"n_total_lines":1208,"dependency_fraction":0.9089403973509934},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000118705","cell_line_id":"CID000184","localizations":[{"compartment":"er","grade":3}],"interactors":[{"gene":"DAD1","stoichiometry":10.0},{"gene":"DDOST","stoichiometry":10.0},{"gene":"KRTCAP2","stoichiometry":10.0},{"gene":"RPN1","stoichiometry":10.0},{"gene":"STT3A","stoichiometry":10.0},{"gene":"EMD","stoichiometry":10.0},{"gene":"POR","stoichiometry":10.0},{"gene":"MLEC","stoichiometry":10.0},{"gene":"STT3B","stoichiometry":10.0},{"gene":"TMPO","stoichiometry":4.0}],"url":"https://opencell.sf.czbiohub.org/target/CID000184","total_profiled":1310},"omim":[{"mim_id":"610650","title":"ADHESION-REGULATING MOLECULE 1; ADRM1","url":"https://www.omim.org/entry/610650"},{"mim_id":"601308","title":"MYELOID TUMOR SUPPRESSOR","url":"https://www.omim.org/entry/601308"},{"mim_id":"600243","title":"DEFENDER AGAINST CELL DEATH 1; DAD1","url":"https://www.omim.org/entry/600243"},{"mim_id":"180490","title":"RIBOPHORIN II; RPN2","url":"https://www.omim.org/entry/180490"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Endoplasmic reticulum","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPN2"},"hgnc":{"alias_symbol":["SWP1","RPNII","RIBIIR","RPN-II"],"prev_symbol":[]},"alphafold":{"accession":"P04844","domains":[{"cath_id":"1.50.10,1.50.10","chopping":"32-268","consensus_level":"high","plddt":94.793,"start":32,"end":268},{"cath_id":"2.60.40,2.60.40","chopping":"273-370","consensus_level":"high","plddt":87.2645,"start":273,"end":370},{"cath_id":"2.60.40,2.60.40","chopping":"374-504","consensus_level":"high","plddt":91.2848,"start":374,"end":504},{"cath_id":"1.10.287","chopping":"573-631","consensus_level":"medium","plddt":92.9737,"start":573,"end":631}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P04844","model_url":"https://alphafold.ebi.ac.uk/files/AF-P04844-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P04844-F1-predicted_aligned_error_v6.png","plddt_mean":89.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPN2","jax_strain_url":"https://www.jax.org/strain/search?query=RPN2"},"sequence":{"accession":"P04844","fasta_url":"https://rest.uniprot.org/uniprotkb/P04844.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P04844/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P04844"}},"corpus_meta":[{"pmid":"18724378","id":"PMC_18724378","title":"RPN2 gene confers docetaxel resistance in breast cancer.","date":"2008","source":"Nature medicine","url":"https://pubmed.ncbi.nlm.nih.gov/18724378","citation_count":135,"is_preprint":false},{"pmid":"24884960","id":"PMC_24884960","title":"RPN2-mediated glycosylation of tetraspanin CD63 regulates breast cancer cell malignancy.","date":"2014","source":"Molecular cancer","url":"https://pubmed.ncbi.nlm.nih.gov/24884960","citation_count":104,"is_preprint":false},{"pmid":"22318722","id":"PMC_22318722","title":"Rpn1 and Rpn2 coordinate ubiquitin processing factors at proteasome.","date":"2012","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/22318722","citation_count":98,"is_preprint":false},{"pmid":"28598414","id":"PMC_28598414","title":"Structure of the Rpn13-Rpn2 complex provides insights for Rpn13 and Uch37 as anticancer targets.","date":"2017","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/28598414","citation_count":73,"is_preprint":false},{"pmid":"12270919","id":"PMC_12270919","title":"What curves alpha-solenoids? Evidence for an alpha-helical toroid structure of Rpn1 and Rpn2 proteins of the 26 S proteasome.","date":"2002","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12270919","citation_count":64,"is_preprint":false},{"pmid":"31888753","id":"PMC_31888753","title":"CircNFIX promotes progression of glioma through regulating miR-378e/RPN2 axis.","date":"2019","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/31888753","citation_count":59,"is_preprint":false},{"pmid":"15210724","id":"PMC_15210724","title":"The bipartite nuclear localization sequence of Rpn2 is required for nuclear import of proteasomal base complexes via karyopherin alphabeta and proteasome functions.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15210724","citation_count":57,"is_preprint":false},{"pmid":"22405010","id":"PMC_22405010","title":"The structure of the 26S proteasome subunit Rpn2 reveals its PC repeat domain as a closed toroid of two concentric α-helical rings.","date":"2012","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/22405010","citation_count":55,"is_preprint":false},{"pmid":"30047227","id":"PMC_30047227","title":"Phytoplasma effector SWP1 induces witches' broom symptom by destabilizing the TCP transcription factor BRANCHED1.","date":"2018","source":"Molecular plant pathology","url":"https://pubmed.ncbi.nlm.nih.gov/30047227","citation_count":49,"is_preprint":false},{"pmid":"28442575","id":"PMC_28442575","title":"Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism.","date":"2017","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/28442575","citation_count":47,"is_preprint":false},{"pmid":"33087705","id":"PMC_33087705","title":"RPN2 is targeted by miR-181c and mediates glioma 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RPN2 modulates its interaction with the ubiquitin receptor RPN13.","date":"2019","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31064842","citation_count":12,"is_preprint":false},{"pmid":"31743606","id":"PMC_31743606","title":"Overexpression of RPN2 promotes osteogenic differentiation of hBMSCs through the JAK/STAT3 pathway.","date":"2019","source":"FEBS open bio","url":"https://pubmed.ncbi.nlm.nih.gov/31743606","citation_count":11,"is_preprint":false},{"pmid":"33330095","id":"PMC_33330095","title":"Lysine in Combination With Estradiol Promote Dissemination of Estrogen Receptor Positive Breast Cancer via Upregulation of U2AF1 and RPN2 Proteins.","date":"2020","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/33330095","citation_count":11,"is_preprint":false},{"pmid":"33613755","id":"PMC_33613755","title":"circ_SMAD2 regulate colorectal cancer cells proliferation through targeting miR-1258/RPN2 signaling 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knockdown of RPN2 reduces CD63 glycosylation and delocalizes CD63, which in turn displaces MDR1 from the cell surface and reduces chemoresistance and invasion in breast cancer cells.\",\n      \"method\": \"siRNA knockdown of RPN2 and CD63, glycosylation assay, co-localization/membrane fractionation, Transwell invasion assay, drug resistance assay\",\n      \"journal\": \"Molecular cancer\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — orthogonal knockdown experiments (RPN2 and CD63 separately), glycosylation assay, functional readouts (invasion, drug resistance), builds on prior validated mechanism\",\n      \"pmids\": [\"24884960\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Yeast Rpn2 (proteasome subunit) directly binds ubiquitin receptor Rpn13 at its C-terminus, and stabilizes the association of Rpn10 with the central solenoid portion of Rpn1, coordinating multiple ubiquitin-processing factors at the 19S regulatory particle.\",\n      \"method\": \"Biochemical binding assays (association/dissociation constants), Co-IP, affinity measurements in yeast proteasome system\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding assays with quantitative affinity measurements, multiple binding partners tested with orthogonal approaches\",\n      \"pmids\": [\"22318722\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The eleven PC repeats of Rpn2 form a closed toroidal structure with two concentric rings of α-helices encircling two axial α-helices; the C-terminal 20 residues of Rpn2 serve as the docking site for ubiquitin receptor Rpn13.\",\n      \"method\": \"X-ray crystallography / structural determination of Rpn2 PC domain; binding assays for Rpn13\",\n      \"journal\": \"Structure (London, England : 1993)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional domain mapping, consistent with independent biochemical data from other labs\",\n      \"pmids\": [\"22405010\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"The bipartite nuclear localization sequence (NLS) of yeast Rpn2 is required for nuclear import of proteasomal base complexes via the karyopherin αβ pathway; deletion of the Rpn2 NLS results in improper nuclear proteasome localization and impaired proteasome function.\",\n      \"method\": \"NLS deletion mutagenesis, karyopherin pathway analysis, nuclear localization assay, proteasome function assay in yeast\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — NLS deletion mutant with direct localization and functional readout, karyopherin dependence established by epistasis\",\n      \"pmids\": [\"15210724\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The C-terminal 14 residues of human RPN2 constitute the binding epitope for RPN13/ADRM1's N-terminal PRU domain; crystal structures of the RPN13 PRU domain in complex with RPN2 C-terminal peptides and ubiquitin were determined, and mutagenesis validated the binding interface. RPN2, ubiquitin, and UCH37 bind RPN13 with independent energetics.\",\n      \"method\": \"Crystal structure determination, surface plasmon resonance, fluorescence polarization, mutational analysis using human proteins\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures plus mutagenesis plus quantitative biophysical binding assays, multiple orthogonal methods in one study\",\n      \"pmids\": [\"28442575\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"A proline-rich C-terminal extension of hRpn2 stretches across a narrow canyon of the ubiquitin-binding Pru domain of hRpn13, blocking an RA190-binding surface; hRpn13 binds preferentially to hRpn2 and proteasomes over the anticancer compound RA190. RA190 does not affect hRpn13–Uch37 interaction but directly binds and inactivates Uch37.\",\n      \"method\": \"Crystal/NMR structure of hRpn13–hRpn2 complex, biophysical binding assays (SPR, ITC), cell-based assays with hRpn13 deletion in HCT116 cells\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — structure of the complex with biophysical validation plus cell-based functional assays, multiple orthogonal methods\",\n      \"pmids\": [\"28598414\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Phosphorylation of RPN2 Tyr-950 (identified in Jurkat cells) enhances RPN2 binding to RPN13; a crystal structure of the RPN2(pTyr-950)–RPN13–ubiquitin complex at 1.76 Å resolution reveals specific interactions with positively charged RPN13 side chains that explain the increased affinity without conformational change.\",\n      \"method\": \"Crystal structure at 1.76 Å, mutagenesis, quantitative binding assays (SPR, fluorescence polarization), phospho-site identification in cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution crystal structure combined with mutagenesis and quantitative biophysical assays\",\n      \"pmids\": [\"31064842\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Sequence analysis and molecular modeling predict that the PC repeat-containing domains of Rpn1/S2 and Rpn2/S1 adopt an α-helical toroid architecture with a central pore, proposed to form an antechamber for unfolded substrates ahead of the ATPase ring.\",\n      \"method\": \"Computational sequence analysis, molecular modeling\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational/modeling study only, no experimental validation in this paper (though later confirmed by crystallography)\",\n      \"pmids\": [\"12270919\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"RPN2 knockdown reduced glycosylation of EGFR, decreased EGFR cell-surface transport, and attenuated EGFR/ERK signaling, thereby inhibiting colorectal cancer cell proliferation in vitro and in vivo.\",\n      \"method\": \"siRNA knockdown, glycosylation assay, EGFR cell-surface transport assay, ERK signaling analysis, in vitro proliferation and in vivo xenograft\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA KD with glycosylation assay and signaling readout, single lab, two orthogonal approaches\",\n      \"pmids\": [\"29069815\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"IEX-1 (immediate early gene-X-1) reduces expression of proteasome subunits S1/Rpn2 and S5a/Rpn10 at the transcriptional level (interference with S5a promoter activity), leading to decreased 26S proteasome assembly and activity in HEK-293 cells.\",\n      \"method\": \"Overexpression of IEX-1 in HEK-293 cells, quantitative RT-PCR, luciferase promoter assay, cycloheximide/actinomycin D chase, 26S proteasome activity assay\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple methods (RT-PCR, promoter assay, drug chase, activity assay) in single lab\",\n      \"pmids\": [\"17107344\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"RPN2 promotes hepatocellular carcinoma cell invasion by activating NF-κB p65 to upregulate MMP-9, and phosphorylated RPN2 activates STAT3, which also upregulates MMP-9 and promotes invasion.\",\n      \"method\": \"RPN2 overexpression and knockdown, western blot for MMP-9/NF-κB/STAT3, immunofluorescence, invasion assays in HCC cells\",\n      \"journal\": \"Aging\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single set of methods, pathway placement based on western blot without rigorous epistasis\",\n      \"pmids\": [\"31481647\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RPN2 knockdown in colon carcinoma cells reduced cell viability, increased apoptosis (caspase-3 upregulation), arrested cell cycle at G0/G1 (cyclin D1 reduction), and inhibited migration/invasion by regulating E-cadherin, MMP-2, and TIMP-2; STAT3 and JAK2 phosphorylation were reduced by RPN2 siRNA.\",\n      \"method\": \"siRNA knockdown, flow cytometry, Transwell assay, western blot, RT-PCR in colon cancer cell lines\",\n      \"journal\": \"Oncology reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, multiple phenotypic readouts but pathway placement (JAK2/STAT3) based on correlation western blots without epistasis\",\n      \"pmids\": [\"29749494\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RPN2 overexpression suppresses radiosensitivity of glioma cells by activating STAT3 signaling, which upregulates MCL1; depletion of RPN2 in radiation-resistant GBM cells sensitizes them to radiation-induced apoptosis.\",\n      \"method\": \"RPN2 overexpression/knockdown, radiation resistance assay, western blot for STAT3/MCL1, apoptosis assay in GBM cell lines\",\n      \"journal\": \"Molecular medicine (Cambridge, Mass.)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, functional readout present but pathway placement relies on western blot correlation without rigorous mechanistic dissection\",\n      \"pmids\": [\"32404045\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The lncRNA WEE2-AS1 promotes RPN2 protein stabilization by preventing CUL2-mediated ubiquitination of RPN2 at K322, thereby activating the PI3K-Akt signaling pathway in glioblastoma cells.\",\n      \"method\": \"Mass spectrometry, RNA pulldown, RIP assay, Co-IP, luciferase reporter, ubiquitination assay identifying K322 as the ubiquitination site, PI3K-Akt pathway analysis\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ubiquitination site identified by MS with functional Co-IP and pathway readout, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"36168628\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"RPN2 overexpression promotes osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) by inducing JAK1 ubiquitination and activating JAK1/STAT3 signaling, promoting nuclear translocation of STAT3; depletion of JAK1 partially rescues the differentiation defect caused by RPN2 silencing.\",\n      \"method\": \"RPN2 overexpression/knockdown, alkaline phosphatase activity, western blot for JAK1/STAT3 phosphorylation and nuclear translocation, epistasis with JAK1 depletion, hBMSC differentiation assay\",\n      \"journal\": \"FEBS open bio\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — epistasis experiment present but mechanistic link between RPN2 and JAK1 ubiquitination lacks rigorous biochemical validation\",\n      \"pmids\": [\"31743606\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM structures of the human 26S proteasome bound to K11/K48-branched ubiquitin chains reveal a novel K11-linked ubiquitin binding site at the groove formed by RPN2 and RPN10, in addition to the canonical K48-linkage binding site; RPN2 recognizes alternating K11-K48 linkages through a conserved motif similar to the K48-specific T1 binding site of RPN1.\",\n      \"method\": \"Cryo-EM structural determination of human 26S proteasome–branched ubiquitin chain complex\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-quality cryo-EM structures but preprint, not yet peer-reviewed; single study\",\n      \"pmids\": [\"bio_10.1101_2025.01.13.632666\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"High-resolution cryo-EM structures of the human 26S proteasome bound to K48-tetraubiquitin and K11/K48-branched chains reveal that K11 branches engage a cleft formed between RPN2 and RPN10; structure-guided mutagenesis confirms these binding modes are essential for efficient substrate degradation and cell cycle progression.\",\n      \"method\": \"Cryo-EM, structure-guided mutagenesis, substrate degradation assay, cell cycle analysis\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM plus mutagenesis plus functional cellular assay, single preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.04.07.647569\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Eleven cryo-EM structures of the human 26S proteasome complexed with ODC reveal that Rpn2's PC domain participates in a multivalent, sequential recognition process for ubiquitin-independent ODC degradation, following initial engagement of the Rpn10 vWA domain and Rpt4/5 coiled-coil.\",\n      \"method\": \"Cryo-EM (11 structures capturing degradation intermediates), structural analysis of proteasome–ODC complex\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — multiple cryo-EM structures but preprint, single study, not peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.11.15.688597\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM structure of TXNL1 bound to the 19S regulatory particle reveals direct interactions between TXNL1 and PSMD1/Rpn2 (as well as Rpn10 and Rpn11), establishing the structural basis for ubiquitin-independent degradation of TXNL1 upon oxidative stress.\",\n      \"method\": \"Cryo-EM structural determination of TXNL1–19S proteasome complex\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 1 / Weak — cryo-EM structure but preprint and single study; RPN2 role inferred from structural contact, not individually validated\",\n      \"pmids\": [\"bio_10.1101_2024.11.08.622741\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RPN2 overexpression in T lymphocytes inhibited apoptosis and IL-4 expression and promoted proliferation and activation, establishing a functional role for RPN2 in T lymphocyte growth and activation.\",\n      \"method\": \"Lentivirus-mediated RPN2 overexpression in T lymphocytes, flow cytometry for apoptosis and proliferation, cytokine measurement (IL-4), activation assays\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, overexpression-only approach, no pathway dissection or mechanistic follow-up\",\n      \"pmids\": [\"34740730\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1991,\n      \"finding\": \"RPN2 (ribophorin II) was chromosomally mapped to human chromosome 20q12-q13.1 by in situ hybridization; the protein was described as a glycoprotein spanning the rough endoplasmic reticulum, proposed to play a role in translocation or maintenance of RER.\",\n      \"method\": \"In situ hybridization chromosomal mapping\",\n      \"journal\": \"Human genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — chromosomal mapping only; functional role is inferred/proposed rather than directly demonstrated\",\n      \"pmids\": [\"2066112\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"Human RPN2 is a core scaffolding subunit of the 19S regulatory particle of the 26S proteasome, whose closed toroidal PC-repeat domain directly recruits ubiquitin receptor RPN13/ADRM1 via its C-terminal residues (with affinity enhanced by phosphorylation of Tyr-950), participates in K11/K48-branched and ubiquitin-independent substrate recognition alongside RPN10, and is required for karyopherin αβ-mediated nuclear import of the base complex; independently, as an obligate subunit of the oligosaccharyltransferase (OST) complex in the ER, RPN2 mediates N-linked glycosylation of substrates including P-glycoprotein/MDR1, CD63, and EGFR, thereby regulating their membrane localization, stability, and downstream signaling, with loss of this glycosylation activity sensitizing cancer cells to chemotherapy.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPN2 is a dual-function protein that operates both as a scaffolding subunit of the 26S proteasome 19S regulatory particle and as a subunit of the ER oligosaccharyltransferase machinery [#3, #0]. Within the 19S particle, its eleven PC repeats fold into a closed α-helical toroid, and the C-terminal residues serve as the docking site that directly recruits the ubiquitin receptor RPN13/ADRM1, with RPN2 also stabilizing the association of RPN10 with the RPN1 solenoid to coordinate ubiquitin-processing factors [#3, #2, #5]. Phosphorylation of RPN2 Tyr-950 enhances the affinity of this RPN13 interaction through specific contacts with positively charged RPN13 residues, without conformational change [#7]. RPN2 contributes to substrate recognition at the proteasome, forming a groove with RPN10 that engages K11/K48-branched ubiquitin chains and participating in ubiquitin-independent degradation of substrates such as ODC [#17, #18], and its bipartite NLS directs karyopherin αβ-mediated nuclear import of the proteasomal base [#4]. Independently, RPN2 mediates N-linked glycosylation of membrane substrates including P-glycoprotein/MDR1, CD63, and EGFR, controlling their cell-surface localization, stability, and signaling; loss of this activity mislocalizes MDR1 and sensitizes chemoresistant cancer cells to therapy [#0, #1, #9].\",\n  \"teleology\": [\n    {\n      \"year\": 1991,\n      \"claim\": \"Established RPN2/ribophorin II as a rough-ER glycoprotein and placed it on the genetic map, the starting point for its ER-associated functions.\",\n      \"evidence\": \"in situ hybridization chromosomal mapping to 20q12-q13.1\",\n      \"pmids\": [\"2066112\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"functional role inferred, not demonstrated\", \"no link to OST activity established here\", \"no proteasomal role identified\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Predicted the architecture of the RPN1/RPN2 PC-repeat domains as α-helical toroids forming an antechamber, framing the structural hypothesis later tested.\",\n      \"evidence\": \"computational sequence analysis and molecular modeling\",\n      \"pmids\": [\"12270919\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"no experimental structure in this work\", \"function of the proposed antechamber untested\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Answered how proteasomal base complexes reach the nucleus by identifying an RPN2 NLS, showing RPN2 has a localization-determining role beyond scaffolding.\",\n      \"evidence\": \"NLS deletion mutagenesis and karyopherin pathway/localization assays in yeast\",\n      \"pmids\": [\"15210724\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"human NLS function not directly tested\", \"regulation of import not addressed\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Showed RPN2 abundance is transcriptionally regulated, linking proteasome assembly to upstream signaling via IEX-1.\",\n      \"evidence\": \"IEX-1 overexpression in HEK-293 with RT-PCR, promoter luciferase, and proteasome activity assays\",\n      \"pmids\": [\"17107344\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"direct promoter binding by IEX-1 not shown\", \"physiological context unclear\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Revealed a chemoresistance function: RPN2 glycosylates MDR1 to maintain its membrane localization, so silencing RPN2 resensitizes resistant tumors.\",\n      \"evidence\": \"siRNA knockdown with glycosylation, membrane localization, apoptosis assays, and xenografts in breast cancer\",\n      \"pmids\": [\"18724378\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"direct enzymatic glycosyltransferase role versus OST-complex dependence not dissected\", \"scope of glycosylated substrates not defined here\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined RPN2's molecular role at the 19S particle by mapping direct RPN13 binding to its C-terminus and showing it stabilizes RPN10, organizing ubiquitin-processing factors.\",\n      \"evidence\": \"quantitative binding assays and Co-IP in yeast plus X-ray crystallography of the PC toroid\",\n      \"pmids\": [\"22318722\", \"22405010\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"human complex interface not yet resolved\", \"functional consequence of RPN13 docking for degradation not measured\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Extended the glycosylation mechanism to CD63, showing RPN2-dependent CD63 glycosylation indirectly controls MDR1 surface display, invasion, and drug resistance.\",\n      \"evidence\": \"orthogonal RPN2 and CD63 knockdowns with glycosylation, fractionation, invasion, and resistance assays\",\n      \"pmids\": [\"24884960\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"mechanism connecting CD63 glycosylation to MDR1 retention unresolved\", \"in vivo validation limited\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Resolved the human RPN2–RPN13 interface at atomic resolution, defining the C-terminal epitope and showing RPN13 binds RPN2, ubiquitin, and UCH37 with independent energetics; also explained why proteasomes outcompete the RA190 inhibitor for RPN13.\",\n      \"evidence\": \"crystal/NMR structures with SPR, ITC, fluorescence polarization, and cell-based assays using human proteins\",\n      \"pmids\": [\"28442575\", \"28598414\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"dynamics of RPN13 recruitment in intact proteasome not captured\", \"therapeutic exploitation untested in vivo here\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Generalized the glycosylation/membrane-localization mechanism to EGFR, linking RPN2 to EGFR/ERK-driven proliferation in colorectal cancer.\",\n      \"evidence\": \"siRNA knockdown with glycosylation, surface transport, ERK signaling, and xenograft assays\",\n      \"pmids\": [\"29069815\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"direct enzymatic role versus OST dependence not separated\", \"single lab\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showed RPN2 phosphorylation tunes proteasome function by demonstrating that pTyr-950 increases RPN13 affinity through defined electrostatic contacts.\",\n      \"evidence\": \"1.76 Å crystal structure of the RPN2(pTyr-950)–RPN13–ubiquitin complex with mutagenesis and biophysical assays\",\n      \"pmids\": [\"31064842\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"kinase responsible for Tyr-950 phosphorylation unidentified\", \"physiological trigger and consequence for degradation unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Reported pro-tumorigenic and differentiation roles for RPN2 via STAT3-axis signaling in HCC and bone marrow stem cells.\",\n      \"evidence\": \"overexpression/knockdown with western blot, immunofluorescence, invasion, and differentiation assays\",\n      \"pmids\": [\"31481647\", \"31743606\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"pathway placement rests on correlative western blots\", \"direct biochemical link between RPN2 and JAK1/STAT3 not validated\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified post-translational control of RPN2 itself: lncRNA WEE2-AS1 blocks CUL2-mediated ubiquitination at K322 to stabilize RPN2 and activate PI3K-Akt signaling.\",\n      \"evidence\": \"MS, RNA pulldown, RIP, Co-IP, ubiquitination assay mapping K322, and pathway analysis in glioblastoma\",\n      \"pmids\": [\"36168628\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"mechanism by which stabilized RPN2 activates PI3K-Akt unclear\", \"single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined the structural basis for branched-chain and ubiquitin-independent substrate recognition, showing RPN2 forms a groove with RPN10 that engages K11/K48-branched ubiquitin and participates in sequential ODC and TXNL1 capture.\",\n      \"evidence\": \"cryo-EM of human 26S proteasome with branched ubiquitin, ODC, and TXNL1, plus structure-guided mutagenesis and degradation/cell-cycle assays (preprints)\",\n      \"pmids\": [\"bio_10.1101_2025.01.13.632666\", \"bio_10.1101_2025.04.07.647569\", \"bio_10.1101_2025.11.15.688597\", \"bio_10.1101_2024.11.08.622741\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"findings are preprints not yet peer-reviewed\", \"RPN2-specific contribution to ODC/TXNL1 degradation inferred from structure\", \"in vivo relevance of branched-chain site untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved whether RPN2's proteasomal scaffolding role and its ER glycosylation role are mechanistically coupled, and which kinases and physiological signals govern RPN2 phosphorylation and stability to switch between these functions.\",\n      \"evidence\": \"no timeline study integrates the two functional contexts\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"no study bridges OST and proteasome roles\", \"upstream regulatory kinases unidentified\", \"tissue-specific functional balance unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 3, 5]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 21]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 9]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [2, 3, 5]}\n    ],\n    \"complexes\": [\n      \"26S proteasome 19S regulatory particle\",\n      \"oligosaccharyltransferase (OST) complex\"\n    ],\n    \"partners\": [\n      \"RPN13/ADRM1\",\n      \"RPN10\",\n      \"RPN1\",\n      \"TXNL1\",\n      \"CUL2\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":5,"faith_total":5,"faith_pct":100.0}}