{"gene":"PF3D7_1414000","run_date":"2026-09-08T19:44:17","timeline":{"discoveries":[{"year":2015,"finding":"PF3D7_1414000 (RPN13/PfRpn13) was identified as an intrinsic ubiquitin receptor of the P. falciparum 26S proteasome; its role in proteasomal substrate recognition was analyzed after affinity purification of functional 26S proteasome complexes from the parasite.","method":"Affinity purification of native 26S proteasome complexes, in situ protein crosslinking, mass spectrometry-based subunit identification","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, proteomic identification of RPN13 as a ubiquitin receptor within the purified proteasome complex, but limited orthogonal mechanistic follow-up on RPN13 specifically","pmids":["26639022"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2020,"finding":"PF3D7_1414000 (PfRpn13) was shown to interact with the shuttle protein PfDsk2 via PfDsk2's UBL domain; the affinity of this interaction was similar in magnitude to the human homolog system, and a novel interaction between the PfRpn13 DEUBAD domain and PfDsk2 UBL was identified, suggesting PfRpn13 may cooperate with deubiquitinating enzymes during substrate proofreading.","method":"Crystal structure of PfDsk2 UBL domain at 1.30 Å resolution; binding affinity measurements (dissociation constants) between PfDsk2 UBL and PfRpn13","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 1–2 / Weak — crystal structure plus binding affinity measurements, but single lab and the RPN13-specific interaction data derive from biochemical binding assays described only in the abstract without full mechanistic dissection of RPN13's function","pmids":["32057831"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"finding":"PF3D7_1414000 (PfRpn13) directly interacts with PfUCH37 via the DEUBAD domain of PfRpn13, which binds the C-terminal region of PfUCH37; deletion of the last 20 amino acids of PfUCH37 (corresponding to human residues 313–329 critical for Rpn13 binding) entirely ablated co-precipitation with PfRpn13, establishing that this interaction mechanism is evolutionarily conserved.","method":"Co-immunoprecipitation using transgenic P. falciparum parasites expressing truncated PfUCH37 constructs; proteomics","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal pull-down with defined truncation mutant plus proteomics in transgenic parasites, single lab but two orthogonal approaches (co-IP and proteomics)","pmids":["39604441"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"finding":"Under complexome profiling conditions, PF3D7_1414000 (RPN13) was NOT found co-migrating with any of the observed 19S or 20S proteasome assemblies in P. falciparum asexual blood stage and gametocyte extracts, suggesting it does not stably associate with these complexes under the experimental conditions used.","method":"Complexome profiling (native mass spectrometry / co-migration profiling across asexual blood stages and gametocytes)","journal":"Nature communications","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single negative finding by complexome profiling, single lab; absence of co-migration may reflect technical conditions rather than true non-association","pmids":["34155201"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1414000 (RPN13/PfRpn13) functions as an intrinsic ubiquitin receptor of the P. falciparum 26S proteasome regulatory particle, where its DEUBAD domain directly binds the shuttle protein PfDsk2 (via PfDsk2's UBL domain) and recruits the deubiquitinase PfUCH37 via a C-terminal interaction that is evolutionarily conserved with the human Rpn13–UCH37 axis, suggesting PfRpn13 coordinates ubiquitinated substrate recognition and deubiquitinase activation at the proteasome."},"narrative":{"mechanistic_narrative":"PF3D7_1414000 (RPN13/PfRpn13) is an intrinsic ubiquitin receptor of the P. falciparum 26S proteasome regulatory particle, identified within affinity-purified native proteasome complexes and implicated in proteasomal substrate recognition [PMID:26639022]. Its DEUBAD domain directly binds the shuttle protein PfDsk2 through PfDsk2's UBL domain, with an affinity comparable to the human homolog system, positioning PfRpn13 to receive ubiquitinated substrates and cooperate with deubiquitinating enzymes during substrate proofreading [PMID:32057831]. The same DEUBAD domain also engages the deubiquitinase PfUCH37 by binding its C-terminal region, and deletion of the last 20 amino acids of PfUCH37 abolishes the interaction, establishing that the Rpn13–UCH37 binding mechanism is evolutionarily conserved in the parasite [PMID:39604441]. Together these findings place PfRpn13 at the interface of ubiquitinated substrate delivery and deubiquitinase recruitment at the proteasome. A complexome profiling study did not detect PfRpn13 co-migrating with 19S or 20S proteasome assemblies in asexual blood-stage or gametocyte extracts [PMID:34155201]; beyond these interaction and localization findings, no functional or genetic characterization of PfRpn13 has been reported in the available corpus.","teleology":[{"year":2015,"claim":"Establishing which subunit of the parasite proteasome recognizes ubiquitinated substrates was needed to map how P. falciparum targets proteins for degradation; this work placed PfRpn13 as an intrinsic ubiquitin receptor of the native 26S proteasome.","evidence":"Affinity purification of native 26S proteasome complexes with in situ crosslinking and mass spectrometry subunit identification in P. falciparum","pmids":["26639022"],"confidence":"Medium","gaps":["No direct binding assay demonstrating PfRpn13 engages ubiquitin or polyubiquitin chains","RPN13-specific role inferred from complex composition rather than isolated functional assay","No genetic evidence for essentiality or phenotype"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2020,"claim":"Whether PfRpn13 physically receives substrate-shuttling factors was unresolved; identifying a DEUBAD-domain interaction with the shuttle protein PfDsk2 UBL domain defined a route for ubiquitinated substrate delivery to the parasite proteasome.","evidence":"Crystal structure of PfDsk2 UBL domain at 1.30 Å plus dissociation-constant measurements between PfDsk2 UBL and PfRpn13","pmids":["32057831"],"confidence":"Medium","gaps":["No co-crystal structure of the PfRpn13–PfDsk2 complex","Functional consequence of the interaction for substrate degradation not tested in parasites","Single lab, binding data reported only at the level described"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"claim":"Whether the conserved Rpn13–UCH37 deubiquitinase axis operates in the parasite was unknown; mapping the DEUBAD-to-C-terminal PfUCH37 interaction and abolishing it by truncation established a conserved mechanism for deubiquitinase recruitment.","evidence":"Co-immunoprecipitation with a defined PfUCH37 C-terminal truncation mutant and proteomics in transgenic P. falciparum parasites","pmids":["39604441"],"confidence":"Medium","gaps":["No demonstration that PfRpn13 binding activates PfUCH37 deubiquitinase activity","Structural basis of the DEUBAD–PfUCH37 interaction not resolved","Functional impact on proteasomal substrate processing not measured"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"claim":"The stability of PfRpn13 association with assembled proteasomes was probed by native co-migration; PfRpn13 was not detected co-migrating with 19S or 20S assemblies, raising the question of how stably it associates under these conditions.","evidence":"Complexome profiling by native co-migration mass spectrometry across asexual blood stages and gametocytes in P. falciparum","pmids":["34155201"],"confidence":"Low","gaps":["Negative result may reflect technical dissociation during native profiling rather than true non-association","Does not distinguish sub-stoichiometric or transient association from absence","Not reconciled with detection of PfRpn13 within purified proteasomes"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether PfRpn13 is essential for parasite viability and how its coordinated recognition of ubiquitinated substrates and recruitment of PfUCH37 alters degradation kinetics or drug susceptibility remains unaddressed.","evidence":"","pmids":[],"confidence":"Low","gaps":["No genetic knockout or knockdown phenotype reported","No demonstration of ubiquitin/polyubiquitin binding activity for PfRpn13 itself","Functional integration of substrate delivery and deubiquitination at the parasite proteasome not established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["26S proteasome regulatory particle (P. falciparum) [#0]"],"partners":["PFDSK2 (UBL DOMAIN) [#1]","PFUCH37 (C-TERMINAL REGION) [#2]"],"other_free_text":["PfRpn13 uses its DEUBAD domain to bind both the shuttle protein PfDsk2 and the deubiquitinase PfUCH37 [#1, #2]","The PfRpn13–PfUCH37 interaction mechanism is evolutionarily conserved with the human Rpn13–UCH37 axis [#2]","PfRpn13 was not detected co-migrating with 19S/20S proteasome assemblies by complexome profiling [#3]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"26639022","id":"PMC_26639022","title":"Characterization of the 26S proteasome network in Plasmodium falciparum.","date":"2015","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/26639022","citation_count":32,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"32057831","id":"PMC_32057831","title":"The recognition of proteasomal receptors by Plasmodium falciparum DSK2.","date":"2020","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/32057831","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfRPN13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39604441","id":"","title":"Proteasome associated function of UCH37 is evolutionarily conserved in Plasmodium parasites.","date":"2024","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/39604441","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPN13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34155201","id":"","title":"Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34155201","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPN13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"32033280","id":"","title":"Proteasome Inhibitors: Harnessing Proteostasis to Combat Disease.","date":"2020","source":"Molecules (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/32033280","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPN13"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6996,"output_tokens":1333,"usd":0.020491,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6221,"output_tokens":2575,"usd":0.04774,"stage2_stop_reason":"end_turn"},"total_usd":0.068231,"stage1_batch_id":"msgbatch_01SRp5hyRc82zNjddxyCCXGk","stage2_batch_id":"msgbatch_01K3BTmBazRo3pRrMvyaPMTY","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"PF3D7_1414000 (RPN13/PfRpn13) was identified as an intrinsic ubiquitin receptor of the P. falciparum 26S proteasome; its role in proteasomal substrate recognition was analyzed after affinity purification of functional 26S proteasome complexes from the parasite.\",\n      \"method\": \"Affinity purification of native 26S proteasome complexes, in situ protein crosslinking, mass spectrometry-based subunit identification\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, proteomic identification of RPN13 as a ubiquitin receptor within the purified proteasome complex, but limited orthogonal mechanistic follow-up on RPN13 specifically\",\n      \"pmids\": [\"26639022\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"PF3D7_1414000 (PfRpn13) was shown to interact with the shuttle protein PfDsk2 via PfDsk2's UBL domain; the affinity of this interaction was similar in magnitude to the human homolog system, and a novel interaction between the PfRpn13 DEUBAD domain and PfDsk2 UBL was identified, suggesting PfRpn13 may cooperate with deubiquitinating enzymes during substrate proofreading.\",\n      \"method\": \"Crystal structure of PfDsk2 UBL domain at 1.30 Å resolution; binding affinity measurements (dissociation constants) between PfDsk2 UBL and PfRpn13\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Weak — crystal structure plus binding affinity measurements, but single lab and the RPN13-specific interaction data derive from biochemical binding assays described only in the abstract without full mechanistic dissection of RPN13's function\",\n      \"pmids\": [\"32057831\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PF3D7_1414000 (PfRpn13) directly interacts with PfUCH37 via the DEUBAD domain of PfRpn13, which binds the C-terminal region of PfUCH37; deletion of the last 20 amino acids of PfUCH37 (corresponding to human residues 313–329 critical for Rpn13 binding) entirely ablated co-precipitation with PfRpn13, establishing that this interaction mechanism is evolutionarily conserved.\",\n      \"method\": \"Co-immunoprecipitation using transgenic P. falciparum parasites expressing truncated PfUCH37 constructs; proteomics\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal pull-down with defined truncation mutant plus proteomics in transgenic parasites, single lab but two orthogonal approaches (co-IP and proteomics)\",\n      \"pmids\": [\"39604441\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Under complexome profiling conditions, PF3D7_1414000 (RPN13) was NOT found co-migrating with any of the observed 19S or 20S proteasome assemblies in P. falciparum asexual blood stage and gametocyte extracts, suggesting it does not stably associate with these complexes under the experimental conditions used.\",\n      \"method\": \"Complexome profiling (native mass spectrometry / co-migration profiling across asexual blood stages and gametocytes)\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single negative finding by complexome profiling, single lab; absence of co-migration may reflect technical conditions rather than true non-association\",\n      \"pmids\": [\"34155201\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1414000 (RPN13/PfRpn13) functions as an intrinsic ubiquitin receptor of the P. falciparum 26S proteasome regulatory particle, where its DEUBAD domain directly binds the shuttle protein PfDsk2 (via PfDsk2's UBL domain) and recruits the deubiquitinase PfUCH37 via a C-terminal interaction that is evolutionarily conserved with the human Rpn13–UCH37 axis, suggesting PfRpn13 coordinates ubiquitinated substrate recognition and deubiquitinase activation at the proteasome.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1414000 (RPN13/PfRpn13) is an intrinsic ubiquitin receptor of the P. falciparum 26S proteasome regulatory particle, identified within affinity-purified native proteasome complexes and implicated in proteasomal substrate recognition [#0]. Its DEUBAD domain directly binds the shuttle protein PfDsk2 through PfDsk2's UBL domain, with an affinity comparable to the human homolog system, positioning PfRpn13 to receive ubiquitinated substrates and cooperate with deubiquitinating enzymes during substrate proofreading [#1]. The same DEUBAD domain also engages the deubiquitinase PfUCH37 by binding its C-terminal region, and deletion of the last 20 amino acids of PfUCH37 abolishes the interaction, establishing that the Rpn13\\u2013UCH37 binding mechanism is evolutionarily conserved in the parasite [#2]. Together these findings place PfRpn13 at the interface of ubiquitinated substrate delivery and deubiquitinase recruitment at the proteasome. A complexome profiling study did not detect PfRpn13 co-migrating with 19S or 20S proteasome assemblies in asexual blood-stage or gametocyte extracts [#3]; beyond these interaction and localization findings, no functional or genetic characterization of PfRpn13 has been reported in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"Establishing which subunit of the parasite proteasome recognizes ubiquitinated substrates was needed to map how P. falciparum targets proteins for degradation; this work placed PfRpn13 as an intrinsic ubiquitin receptor of the native 26S proteasome.\",\n      \"evidence\": \"Affinity purification of native 26S proteasome complexes with in situ crosslinking and mass spectrometry subunit identification in P. falciparum\",\n      \"pmids\": [\"26639022\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct binding assay demonstrating PfRpn13 engages ubiquitin or polyubiquitin chains\",\n        \"RPN13-specific role inferred from complex composition rather than isolated functional assay\",\n        \"No genetic evidence for essentiality or phenotype\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Whether PfRpn13 physically receives substrate-shuttling factors was unresolved; identifying a DEUBAD-domain interaction with the shuttle protein PfDsk2 UBL domain defined a route for ubiquitinated substrate delivery to the parasite proteasome.\",\n      \"evidence\": \"Crystal structure of PfDsk2 UBL domain at 1.30 \\u00c5 plus dissociation-constant measurements between PfDsk2 UBL and PfRpn13\",\n      \"pmids\": [\"32057831\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No co-crystal structure of the PfRpn13\\u2013PfDsk2 complex\",\n        \"Functional consequence of the interaction for substrate degradation not tested in parasites\",\n        \"Single lab, binding data reported only at the level described\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Whether the conserved Rpn13\\u2013UCH37 deubiquitinase axis operates in the parasite was unknown; mapping the DEUBAD-to-C-terminal PfUCH37 interaction and abolishing it by truncation established a conserved mechanism for deubiquitinase recruitment.\",\n      \"evidence\": \"Co-immunoprecipitation with a defined PfUCH37 C-terminal truncation mutant and proteomics in transgenic P. falciparum parasites\",\n      \"pmids\": [\"39604441\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No demonstration that PfRpn13 binding activates PfUCH37 deubiquitinase activity\",\n        \"Structural basis of the DEUBAD\\u2013PfUCH37 interaction not resolved\",\n        \"Functional impact on proteasomal substrate processing not measured\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"The stability of PfRpn13 association with assembled proteasomes was probed by native co-migration; PfRpn13 was not detected co-migrating with 19S or 20S assemblies, raising the question of how stably it associates under these conditions.\",\n      \"evidence\": \"Complexome profiling by native co-migration mass spectrometry across asexual blood stages and gametocytes in P. falciparum\",\n      \"pmids\": [\"34155201\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Negative result may reflect technical dissociation during native profiling rather than true non-association\",\n        \"Does not distinguish sub-stoichiometric or transient association from absence\",\n        \"Not reconciled with detection of PfRpn13 within purified proteasomes\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PfRpn13 is essential for parasite viability and how its coordinated recognition of ubiquitinated substrates and recruitment of PfUCH37 alters degradation kinetics or drug susceptibility remains unaddressed.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No genetic knockout or knockdown phenotype reported\",\n        \"No demonstration of ubiquitin/polyubiquitin binding activity for PfRpn13 itself\",\n        \"Functional integration of substrate delivery and deubiquitination at the parasite proteasome not established\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0043130\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005515\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0000502\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0043161\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"complexes\": [\n      \"26S proteasome regulatory particle (P. falciparum) [#0]\"\n    ],\n    \"partners\": [\n      \"PfDsk2 (UBL domain) [#1]\",\n      \"PfUCH37 (C-terminal region) [#2]\"\n    ],\n    \"other_free_text\": [\n      \"PfRpn13 uses its DEUBAD domain to bind both the shuttle protein PfDsk2 and the deubiquitinase PfUCH37 [#1, #2]\",\n      \"The PfRpn13\\u2013PfUCH37 interaction mechanism is evolutionarily conserved with the human Rpn13\\u2013UCH37 axis [#2]\",\n      \"PfRpn13 was not detected co-migrating with 19S/20S proteasome assemblies by complexome profiling [#3]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1414000","name":null,"product":"26S proteasome regulatory subunit RPN13, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1028700","name":null,"product":"26S proteasome regulatory subunit RPN13, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1344300","name":null,"product":"26S proteasome regulatory subunit RPN13, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RPN13","evaluation":null}