{"gene":"RANBP3","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":1998,"finding":"RanBP3 was identified as a nuclear Ran-binding protein that preferentially binds RanGTP and contains FXFG nucleoporin motifs and a C-terminal RanBP1-like domain; it was localized to the nucleus and proposed to act as a nuclear effector of the Ran pathway.","method":"Yeast two-hybrid, cDNA cloning, subcellular localization by immunofluorescence","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — yeast two-hybrid identification plus biochemical binding assay and localization, single lab but multiple methods","pmids":["9637251"],"is_preprint":false},{"year":1999,"finding":"RanBP3 contains an unusual N-terminal nuclear localization signal (residues 40–57) that is imported preferentially by importin-alpha3 (and alpha4), rather than equivalently by all importin-alpha isoforms as seen with the SV40 T-antigen NLS; nuclear import requires importin-alpha and importin-beta.","method":"Microinjection of GST-GFP-RanBP3 fusions, deletion analysis, recombinant importin-alpha binding assays, competitive inhibition","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (microinjection, deletion mapping, direct binding assays with five importin-alpha isoforms) in a single rigorous study","pmids":["10567565"],"is_preprint":false},{"year":2001,"finding":"RanBP3 interacts directly with CRM1 and forms a trimeric complex with CRM1 and RanGTP; it acts as a cofactor that stabilizes CRM1–export substrate interactions (rather than acting as an export substrate itself) and stimulates CRM1-dependent protein export in permeabilized cells; it also alters the relative affinity of CRM1 for different NES-containing substrates.","method":"In vitro binding assays, permeabilized-cell export assay, co-immunoprecipitation","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro reconstitution of trimeric complex, permeabilized-cell functional assay, and substrate-affinity assay in one study; independently corroborated by structural work","pmids":["11571268"],"is_preprint":false},{"year":2003,"finding":"The CRM1 region comprising residues 411, 414, 474, and 481 constitutes the binding interface for RanBP3; residues 411 and 414 additionally overlap with the domain required for HTLV-1 Rex multimerization, revealing a multifunctional surface on CRM1.","method":"Human/rat CRM1 chimeric mutant analysis, functional Rex multimerization and export assays","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mutagenesis with functional readouts in a single lab study","pmids":["14612415"],"is_preprint":false},{"year":2005,"finding":"RanBP3 directly binds active (dephosphorylated) beta-catenin in a RanGTP-stimulated manner and promotes nuclear export of beta-catenin independently of APC and CRM1; RanBP3 depletion increases nuclear dephosphorylated beta-catenin and Wnt target gene transcription, while overexpression shifts active beta-catenin to the cytoplasm.","method":"Yeast two-hybrid screen with RanGTP marker, direct binding assays, RNAi depletion, overexpression, beta-catenin localization by immunofluorescence, Xenopus and Drosophila epistasis","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct binding confirmed, loss-of-function and gain-of-function with localization readout, validated in three model systems","pmids":["16314428"],"is_preprint":false},{"year":2009,"finding":"RanBP3 directly recognizes dephosphorylated Smad2/3 (produced by nuclear Smad phosphatases) and mediates their nuclear export in a Ran-dependent manner, thereby terminating TGF-beta signaling; depletion of RanBP3 enhances TGF-beta antiproliferative and transcriptional responses, while overexpression inhibits them.","method":"Direct binding assays, co-immunoprecipitation, RNAi knockdown, overexpression, dominant-negative constructs, Xenopus embryo functional assay","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding assays, loss-of-function and gain-of-function with defined signaling readouts, validated in mammalian cells and Xenopus","pmids":["19289081"],"is_preprint":false},{"year":2011,"finding":"Crystal structure of the RanBP3 Ran-binding domain (RBD) reveals structural differences from RanBP1 and RanBP2 RBDs that explain why RanBP3 binds Ran with unusually low affinity, how it modulates CRM1 cargo selectivity, and why it promotes export complex assembly (rather than disassembly as RanBP1/2 do in the cytosol).","method":"X-ray crystallography of RanBP3 RBD, structural comparison with RanBP1/RanBP2 RBD–Ran–CRM1 complexes","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with mechanistic interpretation grounded in comparison to related structures; single lab but high-resolution structural method","pmids":["21364925"],"is_preprint":false},{"year":2011,"finding":"Protein phosphatase PPM1A directly interacts with and dephosphorylates RanBP3 at Ser58 in vitro and in vivo; dephosphorylation at Ser58 enhances the ability of RanBP3 to export Smad2/3 and terminate TGF-beta signaling; RanBP3 phosphorylation is elevated in PPM1A-null MEFs.","method":"In vitro phosphatase assay, co-immunoprecipitation, PPM1A-null MEFs, functional nuclear export assay","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro enzymatic assay with site-specific phosphorylation, genetic null model, and functional export readout","pmids":["21960005"],"is_preprint":false},{"year":2016,"finding":"RanBP3 is required for nuclear export of ERK (a weak-NES cargo) but is dispensable for CRM1-mediated export of strong-NES cargoes; RanBP3 silencing causes ERK nuclear entrapment and increases cytoplasmic non-phosphorylated (active) pro-apoptotic BAD, suggesting ERK nuclear exit depends on RanBP3.","method":"shRNA loss-of-function, NES analysis, immunofluorescence-based protein localization in melanoma cell lines","journal":"The Journal of investigative dermatology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — immunofluorescence localization with RNAi, multiple cell lines, single lab","pmids":["26763446"],"is_preprint":false},{"year":2022,"finding":"Small molecule NU2058 directly targets RanBP3 (identified by LiP-SMap/MS) and increases the RanBP3–beta-catenin interaction, promoting nuclear export of beta-catenin and suppressing transcription of c-Myc and cyclin D1, inducing cell senescence in colorectal cancer cells.","method":"LiP-SMap/mass spectrometry target identification, co-immunoprecipitation, beta-catenin localization, in vitro and in vivo tumor models","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — chemical proteomics target ID plus functional co-IP and localization data in multiple models, single lab","pmids":["36270974"],"is_preprint":false},{"year":2026,"finding":"RANBP3 recruits RAN-GTP to assemble an export-competent quaternary complex (CRM1–HBV RNAs–RANBP3–RAN-GTP) required for nuclear export of HBV RNAs; knockdown of RANBP3 or RAN, or CRM1 mutations blocking cofactor binding, severely impairs HBV RNA export and viral replication.","method":"RNAi knockdown of RANBP3/RAN, CRM1 mutagenesis, RNA export and viral replication assays","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined molecular complex and functional replication readout; single lab, no structural validation","pmids":["42059628"],"is_preprint":false}],"current_model":"RanBP3 is a nuclear Ran-binding protein that functions as a CRM1 cofactor: it binds directly to CRM1 and RanGTP to form a trimeric complex that stabilizes the CRM1–NES cargo interaction and promotes nuclear export of weak-NES cargoes (including ERK, HIV-1 Rev, and HBV RNAs), while independently acting as a direct export receptor for dephosphorylated Smad2/3 (terminating TGF-beta signaling) and for active beta-catenin (dampening Wnt signaling); its export activity is post-translationally regulated by PPM1A-mediated dephosphorylation at Ser58, and its nuclear import is directed by an unusual N-terminal NLS recognized preferentially by importin-alpha3."},"narrative":{"mechanistic_narrative":"RANBP3 is a nuclear Ran-binding protein that operates at the heart of CRM1-dependent nuclear export, acting both as a CRM1 cofactor and as a stand-alone export receptor for specific signaling effectors [PMID:9637251, PMID:11571268]. It binds RanGTP with unusually low affinity and assembles a trimeric complex with CRM1 and RanGTP, where it stabilizes CRM1–NES cargo interactions and reshapes CRM1's affinity for different export substrates rather than serving as a cargo itself [PMID:11571268, PMID:21364925]; structural analysis of its Ran-binding domain explains why RANBP3 promotes export-complex assembly instead of the cytosolic disassembly carried out by RanBP1/RanBP2 [PMID:21364925]. This cofactor role is particularly important for weak-NES cargoes: RANBP3 is required to export ERK while being dispensable for strong-NES substrates [PMID:26763446], and it recruits RanGTP into a quaternary CRM1–HBV RNA–RANBP3–RanGTP complex needed for viral RNA export and replication [PMID:42059628]. Independently of CRM1, RANBP3 directly recognizes dephosphorylated Smad2/3 and exports them to terminate TGF-beta signaling [PMID:19289081], and binds dephosphorylated (active) beta-catenin in a RanGTP-stimulated manner to drive its nuclear exit and dampen Wnt target-gene transcription [PMID:16314428]. Its export activity is regulated by PPM1A, which dephosphorylates RANBP3 at Ser58 to enhance Smad2/3 export [PMID:21960005], and its own nuclear import is directed by an N-terminal NLS preferentially recognized by importin-alpha3 [PMID:10567565]. The small molecule NU2058 targets RANBP3 to enhance its beta-catenin interaction and suppress Wnt-driven proliferation [PMID:36270974].","teleology":[{"year":1998,"claim":"Established RANBP3 as a nuclear member of the Ran pathway, defining the protein's basic identity and RanGTP-preferential binding before any functional role was known.","evidence":"Yeast two-hybrid, cDNA cloning, and immunofluorescence localization","pmids":["9637251"],"confidence":"Medium","gaps":["No functional output of the Ran interaction defined","Whether it acts in import or export unresolved"]},{"year":1999,"claim":"Resolved how the nuclear protein itself reaches the nucleus, identifying an unusual N-terminal NLS with isoform-selective importin-alpha recognition.","evidence":"Microinjection, deletion mapping, and recombinant importin-alpha binding across five isoforms","pmids":["10567565"],"confidence":"High","gaps":["Functional consequence of importin-alpha3 selectivity unknown","No link to regulation of export activity"]},{"year":2001,"claim":"Defined RANBP3's central mechanism as a CRM1 cofactor that stabilizes export complexes and tunes cargo selectivity, distinguishing it from a simple export substrate.","evidence":"In vitro trimeric-complex reconstitution, permeabilized-cell export assay, and substrate-affinity assay","pmids":["11571268"],"confidence":"High","gaps":["Structural basis of assembly-versus-disassembly behavior not yet shown","Physiological cargoes not identified"]},{"year":2003,"claim":"Mapped the CRM1 surface that binds RANBP3 and showed it overlaps a viral-protein interaction site, revealing CRM1 as a multifunctional platform.","evidence":"CRM1 chimeric mutagenesis with Rex multimerization and export functional readouts","pmids":["14612415"],"confidence":"Medium","gaps":["Reciprocal RANBP3 interface residues not mapped","Single-lab functional assays without structural confirmation"]},{"year":2005,"claim":"Identified a CRM1-independent function: RANBP3 acts as a direct export receptor for active beta-catenin, linking it to Wnt signaling control.","evidence":"RanGTP-marker yeast two-hybrid, direct binding, RNAi and overexpression with localization in Xenopus and Drosophila","pmids":["16314428"],"confidence":"High","gaps":["Mechanism of CRM1-independent translocation unclear","How discrimination of dephosphorylated beta-catenin is achieved not defined"]},{"year":2009,"claim":"Extended RANBP3's receptor role to TGF-beta signaling, showing it exports dephosphorylated Smad2/3 to terminate the pathway.","evidence":"Reciprocal binding, co-IP, RNAi, overexpression, dominant-negative constructs, and Xenopus assay","pmids":["19289081"],"confidence":"High","gaps":["Structural basis of dephospho-Smad recognition unknown","Coordination with CRM1-cofactor role not addressed"]},{"year":2011,"claim":"Provided the structural rationale for RANBP3's unique behavior, explaining its low Ran affinity and its promotion of export-complex assembly versus RanBP1/2 disassembly.","evidence":"X-ray crystallography of the RANBP3 Ran-binding domain with comparative structural analysis","pmids":["21364925"],"confidence":"High","gaps":["No structure of full export complex with cargo","Receptor activity toward Smad/beta-catenin not structurally explained"]},{"year":2011,"claim":"Established post-translational regulation of RANBP3, showing PPM1A dephosphorylates Ser58 to enhance Smad2/3 export.","evidence":"In vitro phosphatase assay, co-IP, PPM1A-null MEFs, and functional export readout","pmids":["21960005"],"confidence":"High","gaps":["Kinase responsible for Ser58 phosphorylation not identified","Effect of Ser58 status on CRM1-cofactor activity untested"]},{"year":2016,"claim":"Demonstrated cargo selectivity in vivo: RANBP3 is required for export of weak-NES ERK but not strong-NES cargoes, with downstream consequences for apoptotic signaling.","evidence":"shRNA loss-of-function with immunofluorescence localization in melanoma lines","pmids":["26763446"],"confidence":"Medium","gaps":["Direct ERK–RANBP3 binding not shown","Generality across weak-NES cargoes not tested"]},{"year":2022,"claim":"Showed RANBP3 is a druggable node, with NU2058 enhancing its beta-catenin export activity to suppress Wnt-driven proliferation.","evidence":"LiP-SMap/MS target ID, co-IP, beta-catenin localization, and tumor models","pmids":["36270974"],"confidence":"Medium","gaps":["Binding site of NU2058 on RANBP3 not mapped","Selectivity over other Ran-pathway proteins not established"]},{"year":2026,"claim":"Extended the cofactor function to viral RNA export, showing RANBP3 recruits RanGTP into a quaternary complex required for HBV RNA export and replication.","evidence":"RNAi of RANBP3/RAN, CRM1 mutagenesis, and RNA export and replication assays","pmids":["42059628"],"confidence":"Medium","gaps":["No structural validation of the quaternary complex","Direct RANBP3–HBV RNA contacts not defined"]},{"year":null,"claim":"How RANBP3 mechanistically switches between its CRM1-cofactor mode and its CRM1-independent receptor mode, and how phosphorylation state coordinates these activities, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of a cargo-bound receptor complex","Kinase setting Ser58 phosphorylation unidentified","Integration of cofactor and receptor roles in vivo unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,2,6]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,6]},{"term_id":"GO:0140104","term_label":"molecular carrier activity","supporting_discovery_ids":[4,5]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,4,5]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,1]}],"pathway":[{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[2,4,5,10]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[4,5,8]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[10]}],"complexes":["CRM1–RanGTP–RanBP3 export complex"],"partners":["XPO1","RAN","KPNA4","CTNNB1","SMAD2","SMAD3","PPM1A","MAPK1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H6Z4","full_name":"Ran-binding protein 3","aliases":[],"length_aa":567,"mass_kda":60.2,"function":"Acts as a cofactor for XPO1/CRM1-mediated nuclear export, perhaps as export complex scaffolding protein. Bound to XPO1/CRM1, stabilizes the XPO1/CRM1-cargo interaction. In the absence of Ran-bound GTP prevents binding of XPO1/CRM1 to the nuclear pore complex. Binds to CHC1/RCC1 and increases the guanine nucleotide exchange activity of CHC1/RCC1. Recruits XPO1/CRM1 to CHC1/RCC1 in a Ran-dependent manner. Negative regulator of TGF-beta signaling through interaction with the R-SMAD proteins, SMAD2 and SMAD3, and mediating their nuclear export","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9H6Z4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RANBP3","classification":"Not Classified","n_dependent_lines":347,"n_total_lines":1208,"dependency_fraction":0.28725165562913907},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"XPO1","stoichiometry":10.0},{"gene":"RANGRF","stoichiometry":0.2},{"gene":"SAR1B","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RANBP3","total_profiled":1310},"omim":[{"mim_id":"616391","title":"RAN-BINDING PROTEIN 3-LIKE; RANBP3L","url":"https://www.omim.org/entry/616391"},{"mim_id":"603327","title":"RAN-BINDING PROTEIN 3; RANBP3","url":"https://www.omim.org/entry/603327"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RANBP3"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q9H6Z4","domains":[{"cath_id":"2.30.29.30","chopping":"400-521","consensus_level":"high","plddt":95.4939,"start":400,"end":521}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H6Z4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H6Z4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H6Z4-F1-predicted_aligned_error_v6.png","plddt_mean":61.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RANBP3","jax_strain_url":"https://www.jax.org/strain/search?query=RANBP3"},"sequence":{"accession":"Q9H6Z4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H6Z4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H6Z4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H6Z4"}},"corpus_meta":[{"pmid":"11571268","id":"PMC_11571268","title":"RanBP3 influences interactions between CRM1 and its nuclear protein export substrates.","date":"2001","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/11571268","citation_count":95,"is_preprint":false},{"pmid":"19289081","id":"PMC_19289081","title":"Nuclear export of Smad2 and Smad3 by RanBP3 facilitates termination of TGF-beta signaling.","date":"2009","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/19289081","citation_count":87,"is_preprint":false},{"pmid":"16314428","id":"PMC_16314428","title":"RanBP3 enhances nuclear export of active (beta)-catenin independently of CRM1.","date":"2005","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/16314428","citation_count":79,"is_preprint":false},{"pmid":"10567565","id":"PMC_10567565","title":"RanBP3 contains an unusual nuclear localization signal that is imported preferentially by importin-alpha3.","date":"1999","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10567565","citation_count":69,"is_preprint":false},{"pmid":"9637251","id":"PMC_9637251","title":"Human RanBP3, a group of nuclear RanGTP binding proteins.","date":"1998","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/9637251","citation_count":59,"is_preprint":false},{"pmid":"14612415","id":"PMC_14612415","title":"A multifunctional domain in human CRM1 (exportin 1) mediates RanBP3 binding and multimerization of human T-cell leukemia virus type 1 Rex protein.","date":"2003","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/14612415","citation_count":30,"is_preprint":false},{"pmid":"21960005","id":"PMC_21960005","title":"PPM1A dephosphorylates RanBP3 to enable efficient nuclear export of Smad2 and Smad3.","date":"2011","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/21960005","citation_count":28,"is_preprint":false},{"pmid":"36270974","id":"PMC_36270974","title":"Blockade of Nuclear β-Catenin Signaling via Direct Targeting of RanBP3 with NU2058 Induces Cell Senescence to Suppress Colorectal Tumorigenesis.","date":"2022","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/36270974","citation_count":23,"is_preprint":false},{"pmid":"21364925","id":"PMC_21364925","title":"Insights into the function of the CRM1 cofactor RanBP3 from the structure of its Ran-binding domain.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21364925","citation_count":16,"is_preprint":false},{"pmid":"26763446","id":"PMC_26763446","title":"RanBP3 Regulates Melanoma Cell Proliferation via Selective Control of Nuclear Export.","date":"2016","source":"The Journal of investigative dermatology","url":"https://pubmed.ncbi.nlm.nih.gov/26763446","citation_count":7,"is_preprint":false},{"pmid":"34504783","id":"PMC_34504783","title":"RanBP3 Regulates Proliferation, Apoptosis and Chemosensitivity of Chronic Myeloid Leukemia Cells via Mediating SMAD2/3 and ERK1/2 Nuclear Transport.","date":"2021","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34504783","citation_count":4,"is_preprint":false},{"pmid":"39139156","id":"PMC_39139156","title":"Value of altered methylation patterns of genes RANBP3, LCP2 and GRAP2 in cfDNA in breast cancer diagnosis.","date":"2024","source":"Journal of medical biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/39139156","citation_count":3,"is_preprint":false},{"pmid":"42059628","id":"PMC_42059628","title":"RANBP3 and RAN orchestrate CRM1-mediated nuclear export of hepatitis B virus RNAs.","date":"2026","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/42059628","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8181,"output_tokens":2822,"usd":0.033437,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10006,"output_tokens":3502,"usd":0.06879,"stage2_stop_reason":"end_turn"},"total_usd":0.102227,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1998,\n      \"finding\": \"RanBP3 was identified as a nuclear Ran-binding protein that preferentially binds RanGTP and contains FXFG nucleoporin motifs and a C-terminal RanBP1-like domain; it was localized to the nucleus and proposed to act as a nuclear effector of the Ran pathway.\",\n      \"method\": \"Yeast two-hybrid, cDNA cloning, subcellular localization by immunofluorescence\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — yeast two-hybrid identification plus biochemical binding assay and localization, single lab but multiple methods\",\n      \"pmids\": [\"9637251\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"RanBP3 contains an unusual N-terminal nuclear localization signal (residues 40–57) that is imported preferentially by importin-alpha3 (and alpha4), rather than equivalently by all importin-alpha isoforms as seen with the SV40 T-antigen NLS; nuclear import requires importin-alpha and importin-beta.\",\n      \"method\": \"Microinjection of GST-GFP-RanBP3 fusions, deletion analysis, recombinant importin-alpha binding assays, competitive inhibition\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (microinjection, deletion mapping, direct binding assays with five importin-alpha isoforms) in a single rigorous study\",\n      \"pmids\": [\"10567565\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"RanBP3 interacts directly with CRM1 and forms a trimeric complex with CRM1 and RanGTP; it acts as a cofactor that stabilizes CRM1–export substrate interactions (rather than acting as an export substrate itself) and stimulates CRM1-dependent protein export in permeabilized cells; it also alters the relative affinity of CRM1 for different NES-containing substrates.\",\n      \"method\": \"In vitro binding assays, permeabilized-cell export assay, co-immunoprecipitation\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro reconstitution of trimeric complex, permeabilized-cell functional assay, and substrate-affinity assay in one study; independently corroborated by structural work\",\n      \"pmids\": [\"11571268\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"The CRM1 region comprising residues 411, 414, 474, and 481 constitutes the binding interface for RanBP3; residues 411 and 414 additionally overlap with the domain required for HTLV-1 Rex multimerization, revealing a multifunctional surface on CRM1.\",\n      \"method\": \"Human/rat CRM1 chimeric mutant analysis, functional Rex multimerization and export assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mutagenesis with functional readouts in a single lab study\",\n      \"pmids\": [\"14612415\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"RanBP3 directly binds active (dephosphorylated) beta-catenin in a RanGTP-stimulated manner and promotes nuclear export of beta-catenin independently of APC and CRM1; RanBP3 depletion increases nuclear dephosphorylated beta-catenin and Wnt target gene transcription, while overexpression shifts active beta-catenin to the cytoplasm.\",\n      \"method\": \"Yeast two-hybrid screen with RanGTP marker, direct binding assays, RNAi depletion, overexpression, beta-catenin localization by immunofluorescence, Xenopus and Drosophila epistasis\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct binding confirmed, loss-of-function and gain-of-function with localization readout, validated in three model systems\",\n      \"pmids\": [\"16314428\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"RanBP3 directly recognizes dephosphorylated Smad2/3 (produced by nuclear Smad phosphatases) and mediates their nuclear export in a Ran-dependent manner, thereby terminating TGF-beta signaling; depletion of RanBP3 enhances TGF-beta antiproliferative and transcriptional responses, while overexpression inhibits them.\",\n      \"method\": \"Direct binding assays, co-immunoprecipitation, RNAi knockdown, overexpression, dominant-negative constructs, Xenopus embryo functional assay\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding assays, loss-of-function and gain-of-function with defined signaling readouts, validated in mammalian cells and Xenopus\",\n      \"pmids\": [\"19289081\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Crystal structure of the RanBP3 Ran-binding domain (RBD) reveals structural differences from RanBP1 and RanBP2 RBDs that explain why RanBP3 binds Ran with unusually low affinity, how it modulates CRM1 cargo selectivity, and why it promotes export complex assembly (rather than disassembly as RanBP1/2 do in the cytosol).\",\n      \"method\": \"X-ray crystallography of RanBP3 RBD, structural comparison with RanBP1/RanBP2 RBD–Ran–CRM1 complexes\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with mechanistic interpretation grounded in comparison to related structures; single lab but high-resolution structural method\",\n      \"pmids\": [\"21364925\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Protein phosphatase PPM1A directly interacts with and dephosphorylates RanBP3 at Ser58 in vitro and in vivo; dephosphorylation at Ser58 enhances the ability of RanBP3 to export Smad2/3 and terminate TGF-beta signaling; RanBP3 phosphorylation is elevated in PPM1A-null MEFs.\",\n      \"method\": \"In vitro phosphatase assay, co-immunoprecipitation, PPM1A-null MEFs, functional nuclear export assay\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro enzymatic assay with site-specific phosphorylation, genetic null model, and functional export readout\",\n      \"pmids\": [\"21960005\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"RanBP3 is required for nuclear export of ERK (a weak-NES cargo) but is dispensable for CRM1-mediated export of strong-NES cargoes; RanBP3 silencing causes ERK nuclear entrapment and increases cytoplasmic non-phosphorylated (active) pro-apoptotic BAD, suggesting ERK nuclear exit depends on RanBP3.\",\n      \"method\": \"shRNA loss-of-function, NES analysis, immunofluorescence-based protein localization in melanoma cell lines\",\n      \"journal\": \"The Journal of investigative dermatology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — immunofluorescence localization with RNAi, multiple cell lines, single lab\",\n      \"pmids\": [\"26763446\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Small molecule NU2058 directly targets RanBP3 (identified by LiP-SMap/MS) and increases the RanBP3–beta-catenin interaction, promoting nuclear export of beta-catenin and suppressing transcription of c-Myc and cyclin D1, inducing cell senescence in colorectal cancer cells.\",\n      \"method\": \"LiP-SMap/mass spectrometry target identification, co-immunoprecipitation, beta-catenin localization, in vitro and in vivo tumor models\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — chemical proteomics target ID plus functional co-IP and localization data in multiple models, single lab\",\n      \"pmids\": [\"36270974\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"RANBP3 recruits RAN-GTP to assemble an export-competent quaternary complex (CRM1–HBV RNAs–RANBP3–RAN-GTP) required for nuclear export of HBV RNAs; knockdown of RANBP3 or RAN, or CRM1 mutations blocking cofactor binding, severely impairs HBV RNA export and viral replication.\",\n      \"method\": \"RNAi knockdown of RANBP3/RAN, CRM1 mutagenesis, RNA export and viral replication assays\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined molecular complex and functional replication readout; single lab, no structural validation\",\n      \"pmids\": [\"42059628\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RanBP3 is a nuclear Ran-binding protein that functions as a CRM1 cofactor: it binds directly to CRM1 and RanGTP to form a trimeric complex that stabilizes the CRM1–NES cargo interaction and promotes nuclear export of weak-NES cargoes (including ERK, HIV-1 Rev, and HBV RNAs), while independently acting as a direct export receptor for dephosphorylated Smad2/3 (terminating TGF-beta signaling) and for active beta-catenin (dampening Wnt signaling); its export activity is post-translationally regulated by PPM1A-mediated dephosphorylation at Ser58, and its nuclear import is directed by an unusual N-terminal NLS recognized preferentially by importin-alpha3.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RANBP3 is a nuclear Ran-binding protein that operates at the heart of CRM1-dependent nuclear export, acting both as a CRM1 cofactor and as a stand-alone export receptor for specific signaling effectors [#0, #2]. It binds RanGTP with unusually low affinity and assembles a trimeric complex with CRM1 and RanGTP, where it stabilizes CRM1–NES cargo interactions and reshapes CRM1's affinity for different export substrates rather than serving as a cargo itself [#2, #6]; structural analysis of its Ran-binding domain explains why RANBP3 promotes export-complex assembly instead of the cytosolic disassembly carried out by RanBP1/RanBP2 [#6]. This cofactor role is particularly important for weak-NES cargoes: RANBP3 is required to export ERK while being dispensable for strong-NES substrates [#8], and it recruits RanGTP into a quaternary CRM1–HBV RNA–RANBP3–RanGTP complex needed for viral RNA export and replication [#10]. Independently of CRM1, RANBP3 directly recognizes dephosphorylated Smad2/3 and exports them to terminate TGF-beta signaling [#5], and binds dephosphorylated (active) beta-catenin in a RanGTP-stimulated manner to drive its nuclear exit and dampen Wnt target-gene transcription [#4]. Its export activity is regulated by PPM1A, which dephosphorylates RANBP3 at Ser58 to enhance Smad2/3 export [#7], and its own nuclear import is directed by an N-terminal NLS preferentially recognized by importin-alpha3 [#1]. The small molecule NU2058 targets RANBP3 to enhance its beta-catenin interaction and suppress Wnt-driven proliferation [#9].\",\n  \"teleology\": [\n    {\n      \"year\": 1998,\n      \"claim\": \"Established RANBP3 as a nuclear member of the Ran pathway, defining the protein's basic identity and RanGTP-preferential binding before any functional role was known.\",\n      \"evidence\": \"Yeast two-hybrid, cDNA cloning, and immunofluorescence localization\",\n      \"pmids\": [\"9637251\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional output of the Ran interaction defined\", \"Whether it acts in import or export unresolved\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Resolved how the nuclear protein itself reaches the nucleus, identifying an unusual N-terminal NLS with isoform-selective importin-alpha recognition.\",\n      \"evidence\": \"Microinjection, deletion mapping, and recombinant importin-alpha binding across five isoforms\",\n      \"pmids\": [\"10567565\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of importin-alpha3 selectivity unknown\", \"No link to regulation of export activity\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Defined RANBP3's central mechanism as a CRM1 cofactor that stabilizes export complexes and tunes cargo selectivity, distinguishing it from a simple export substrate.\",\n      \"evidence\": \"In vitro trimeric-complex reconstitution, permeabilized-cell export assay, and substrate-affinity assay\",\n      \"pmids\": [\"11571268\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of assembly-versus-disassembly behavior not yet shown\", \"Physiological cargoes not identified\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Mapped the CRM1 surface that binds RANBP3 and showed it overlaps a viral-protein interaction site, revealing CRM1 as a multifunctional platform.\",\n      \"evidence\": \"CRM1 chimeric mutagenesis with Rex multimerization and export functional readouts\",\n      \"pmids\": [\"14612415\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reciprocal RANBP3 interface residues not mapped\", \"Single-lab functional assays without structural confirmation\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Identified a CRM1-independent function: RANBP3 acts as a direct export receptor for active beta-catenin, linking it to Wnt signaling control.\",\n      \"evidence\": \"RanGTP-marker yeast two-hybrid, direct binding, RNAi and overexpression with localization in Xenopus and Drosophila\",\n      \"pmids\": [\"16314428\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of CRM1-independent translocation unclear\", \"How discrimination of dephosphorylated beta-catenin is achieved not defined\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Extended RANBP3's receptor role to TGF-beta signaling, showing it exports dephosphorylated Smad2/3 to terminate the pathway.\",\n      \"evidence\": \"Reciprocal binding, co-IP, RNAi, overexpression, dominant-negative constructs, and Xenopus assay\",\n      \"pmids\": [\"19289081\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of dephospho-Smad recognition unknown\", \"Coordination with CRM1-cofactor role not addressed\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Provided the structural rationale for RANBP3's unique behavior, explaining its low Ran affinity and its promotion of export-complex assembly versus RanBP1/2 disassembly.\",\n      \"evidence\": \"X-ray crystallography of the RANBP3 Ran-binding domain with comparative structural analysis\",\n      \"pmids\": [\"21364925\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structure of full export complex with cargo\", \"Receptor activity toward Smad/beta-catenin not structurally explained\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Established post-translational regulation of RANBP3, showing PPM1A dephosphorylates Ser58 to enhance Smad2/3 export.\",\n      \"evidence\": \"In vitro phosphatase assay, co-IP, PPM1A-null MEFs, and functional export readout\",\n      \"pmids\": [\"21960005\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Kinase responsible for Ser58 phosphorylation not identified\", \"Effect of Ser58 status on CRM1-cofactor activity untested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Demonstrated cargo selectivity in vivo: RANBP3 is required for export of weak-NES ERK but not strong-NES cargoes, with downstream consequences for apoptotic signaling.\",\n      \"evidence\": \"shRNA loss-of-function with immunofluorescence localization in melanoma lines\",\n      \"pmids\": [\"26763446\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ERK–RANBP3 binding not shown\", \"Generality across weak-NES cargoes not tested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showed RANBP3 is a druggable node, with NU2058 enhancing its beta-catenin export activity to suppress Wnt-driven proliferation.\",\n      \"evidence\": \"LiP-SMap/MS target ID, co-IP, beta-catenin localization, and tumor models\",\n      \"pmids\": [\"36270974\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding site of NU2058 on RANBP3 not mapped\", \"Selectivity over other Ran-pathway proteins not established\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Extended the cofactor function to viral RNA export, showing RANBP3 recruits RanGTP into a quaternary complex required for HBV RNA export and replication.\",\n      \"evidence\": \"RNAi of RANBP3/RAN, CRM1 mutagenesis, and RNA export and replication assays\",\n      \"pmids\": [\"42059628\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural validation of the quaternary complex\", \"Direct RANBP3–HBV RNA contacts not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RANBP3 mechanistically switches between its CRM1-cofactor mode and its CRM1-independent receptor mode, and how phosphorylation state coordinates these activities, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of a cargo-bound receptor complex\", \"Kinase setting Ser58 phosphorylation unidentified\", \"Integration of cofactor and receptor roles in vivo unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 2, 6]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 6]},\n      {\"term_id\": \"GO:0140104\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 4, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [2, 4, 5, 10]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [4, 5, 8]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [10]}\n    ],\n    \"complexes\": [\n      \"CRM1–RanGTP–RanBP3 export complex\"\n    ],\n    \"partners\": [\n      \"XPO1\",\n      \"RAN\",\n      \"KPNA4\",\n      \"CTNNB1\",\n      \"SMAD2\",\n      \"SMAD3\",\n      \"PPM1A\",\n      \"MAPK1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}