{"gene":"PF3D7_0807800","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2015,"finding":"PfRPN10 (PF08_0109) contains two ubiquitin-interacting motif (UIM) domains; in vitro pull-down assays showed that PfUIM2 (and PfUIM1+2 together) efficiently bind both K48- and K63-linked polyubiquitin chains and pull down a broad range of ubiquitin conjugates from P. falciparum extracts, whereas PfUIM1 alone does not bind. This establishes PfRPN10's UIM2 as the functional ubiquitin receptor domain responsible for direct recognition of ubiquitinated substrates by the plasmodial proteasome.","method":"In silico domain analysis followed by recombinant protein expression and Ni-NTA pull-down assays with K48- and K63-linked polyubiquitin chains and P. falciparum cell extracts","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean biochemical pull-down with defined substrates and domain-specific constructs, two orthogonal approaches (synthetic Ub chains and parasite extracts), single lab","pmids":["26639022"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2020,"finding":"PfRPN10 acts as a proteasomal receptor for the shuttle protein PfDsk2; the UBL domain of PfDsk2 interacts with PfRPN10 with a dissociation constant of similar order of magnitude to the human system. Crystal structure of unbound PfDsk2 UBL (1.30 Å) revealed structural differences at the putative binding interface with PfRPN10 compared to the human homolog, but the binding affinity was maintained. This places PfRPN10 as the proteasomal docking site for ubiquitinated-substrate shuttle proteins in P. falciparum.","method":"Crystal structure determination of PfDsk2 UBL domain (1.30 Å resolution) combined with binding affinity measurements (dissociation constants) for the PfDsk2–PfRPN10 interaction","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — crystal structure plus affinity measurements, but single lab and binding interface with PfRPN10 inferred from structural comparison rather than direct mutagenesis of PfRPN10 itself","pmids":["32057831"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"In a Xenopus oocyte heterologous model, P. berghei Rpt3 (PbRpt3) was immunoprecipitated with an anti-Xenopus RPN10 antibody, demonstrating that PbRpt3 can be incorporated into the 19S regulatory particle complex that contains RPN10. Importantly, PP1c was NOT co-precipitated in this RPN10-containing complex, indicating that the Rpt3–PP1c interaction occurs outside the proteasome and is not part of the RPN10-associated 19S assembly.","method":"Co-immunoprecipitation with anti-Xenopus RPN10 antibody in a Xenopus oocyte heterologous expression system","journal":"International journal of molecular sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP in a heterologous system; the result places RPN10 in a 19S complex with PbRpt3 but only indirectly characterizes RPN10's role; single lab, single method","pmids":["41373862"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"P. falciparum RPN10 (PF3D7_0807800) is a subunit of the 19S regulatory particle of the 26S proteasome that functions as an intrinsic ubiquitin receptor: its second UIM domain (UIM2) directly binds K48- and K63-linked polyubiquitin chains and ubiquitinated substrates in vitro, and it serves as the proteasomal docking site for the substrate-shuttle protein PfDsk2 via interaction with PfDsk2's UBL domain."},"narrative":{"mechanistic_narrative":"RPN10 (PF3D7_0807800) is a subunit of the 19S regulatory particle of the Plasmodium 26S proteasome that functions as an intrinsic ubiquitin receptor for the degradation machinery [PMID:26639022]. It carries two ubiquitin-interacting motif (UIM) domains, of which UIM2 is the functional receptor: in vitro, PfUIM2 (alone or in combination with UIM1) binds both K48- and K63-linked polyubiquitin chains and pulls down a broad range of ubiquitin conjugates from parasite extracts, whereas UIM1 alone does not bind [PMID:26639022]. Beyond direct chain recognition, RPN10 serves as the proteasomal docking site for the substrate-shuttle protein PfDsk2, binding the PfDsk2 UBL domain with an affinity comparable to the human system despite structural differences at the interface [PMID:32057831]. In a Xenopus oocyte heterologous system, RPN10 is found in a 19S assembly containing P. berghei Rpt3 but lacking PP1c, indicating the Rpt3–PP1c interaction occurs outside the RPN10-associated regulatory particle [PMID:41373862].","teleology":[{"year":2015,"claim":"It was unknown how the plasmodial proteasome recognizes ubiquitinated substrates; this work established RPN10 as the intrinsic ubiquitin receptor and pinpointed UIM2 as the responsible domain.","evidence":"Recombinant domain-specific constructs in Ni-NTA pull-down assays with K48/K63 polyubiquitin chains and P. falciparum extracts","pmids":["26639022"],"confidence":"Medium","gaps":["No structure of the RPN10 UIM–ubiquitin complex","In vitro binding not linked to substrate turnover in intact parasites","Functional distinction between UIM1 and UIM2 in vivo not tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2020,"claim":"Whether Plasmodium uses shuttle factors to deliver substrates to the proteasome was open; this work showed RPN10 is the docking site for the PfDsk2 shuttle protein via its UBL domain.","evidence":"1.30 Å crystal structure of PfDsk2 UBL plus dissociation-constant measurements of the PfDsk2–RPN10 interaction","pmids":["32057831"],"confidence":"Medium","gaps":["Binding interface inferred from structural comparison rather than direct RPN10 mutagenesis","No co-structure of the RPN10–PfDsk2 complex","Physiological consequence of the shuttle interaction not tested in parasites"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"The composition of the Rpt3-containing 19S particle relative to PP1c was unclear; this work placed RPN10 in a 19S assembly with Rpt3 that excludes PP1c, localizing the Rpt3–PP1c interaction outside the proteasome.","evidence":"Co-immunoprecipitation with anti-Xenopus RPN10 antibody in a Xenopus oocyte heterologous expression system (P. berghei Rpt3)","pmids":["41373862"],"confidence":"Low","gaps":["Single Co-IP in a heterologous system, not validated in Plasmodium","Only indirectly characterizes RPN10's own role","No reciprocal IP or native complex confirmation"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"The in vivo requirement of RPN10 for parasite proteasome function, its essentiality, and the cellular consequences of disrupting its ubiquitin-receptor or shuttle-docking activities remain uncharacterized in the available corpus.","evidence":"","pmids":[],"confidence":"Low","gaps":["No genetic knockdown/knockout phenotype for RPN10 in Plasmodium","No structural model of RPN10 itself","Contribution of RPN10 to antimalarial proteasome-inhibitor sensitivity unknown"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["26S proteasome 19S regulatory particle"],"partners":["PFDSK2 (VIA ITS UBL DOMAIN)","K48- AND K63-LINKED POLYUBIQUITIN CHAINS","RPT3 (IN A XENOPUS HETEROLOGOUS 19S ASSEMBLY)"],"other_free_text":["RPN10 contains two UIM domains; UIM2 is the functional ubiquitin-binding domain while UIM1 alone does not bind [#0]","The PfDsk2–RPN10 interface differs structurally from the human homolog yet retains comparable binding affinity [#1]","PP1c is excluded from the RPN10-containing 19S assembly, placing the Rpt3–PP1c interaction outside the proteasome [#2]"]}},"prefetch_data":{},"corpus_meta":[{"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":["PfRPN10"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41373862","id":"","title":"Characterization of the Regulatory AAA-ATPase Subunit Rpt3 in Plasmodium berghei as an Activator of Protein Phosphatase 1.","date":"2025","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41373862","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPN10"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39497850","id":"","title":"Ubiquitin-proteasome system in Plasmodium: a potential antimalarial target to overcome resistance - a systematic review.","date":"2024","source":"Frontiers in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/39497850","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPN10"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40278767","id":"","title":"Combating Malaria: Targeting the Ubiquitin-Proteasome System to Conquer Drug Resistance.","date":"2025","source":"Tropical medicine and infectious disease","url":"https://pubmed.ncbi.nlm.nih.gov/40278767","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPN10"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38404287","id":"","title":"Mutation in the 26S proteasome regulatory subunit rpn2 gene in Plasmodium falciparum confers resistance to artemisinin.","date":"2024","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/38404287","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPN10"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26639022","id":"","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":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPN10"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"29258508","id":"","title":"Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia.","date":"2017","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/29258508","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPN10"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"28852696","id":"","title":"The Proteasome in Modern Drug Discovery: Second Life of a Highly Valuable Drug Target.","date":"2017","source":"ACS central science","url":"https://pubmed.ncbi.nlm.nih.gov/28852696","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPN10"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26090380","id":"","title":"Role of the Ubiquitin-Proteasome Systems in the Biology and Virulence of Protozoan Parasites.","date":"2015","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/26090380","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPN10"],"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":["RPN10"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25943340","id":"","title":"Evolution of proteasome regulators in eukaryotes.","date":"2015","source":"Genome biology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/25943340","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPN10"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14382,"output_tokens":1199,"usd":0.030565,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6020,"output_tokens":2188,"usd":0.0424,"stage2_stop_reason":"end_turn"},"total_usd":0.072965,"stage1_batch_id":"msgbatch_01NE1MTa8x1hW7Lo4tAaNzY1","stage2_batch_id":"msgbatch_0141vaQdeFvbo2q39AinvXM9","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"PfRPN10 (PF08_0109) contains two ubiquitin-interacting motif (UIM) domains; in vitro pull-down assays showed that PfUIM2 (and PfUIM1+2 together) efficiently bind both K48- and K63-linked polyubiquitin chains and pull down a broad range of ubiquitin conjugates from P. falciparum extracts, whereas PfUIM1 alone does not bind. This establishes PfRPN10's UIM2 as the functional ubiquitin receptor domain responsible for direct recognition of ubiquitinated substrates by the plasmodial proteasome.\",\n      \"method\": \"In silico domain analysis followed by recombinant protein expression and Ni-NTA pull-down assays with K48- and K63-linked polyubiquitin chains and P. falciparum cell extracts\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean biochemical pull-down with defined substrates and domain-specific constructs, two orthogonal approaches (synthetic Ub chains and parasite extracts), single lab\",\n      \"pmids\": [\"26639022\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"PfRPN10 acts as a proteasomal receptor for the shuttle protein PfDsk2; the UBL domain of PfDsk2 interacts with PfRPN10 with a dissociation constant of similar order of magnitude to the human system. Crystal structure of unbound PfDsk2 UBL (1.30 Å) revealed structural differences at the putative binding interface with PfRPN10 compared to the human homolog, but the binding affinity was maintained. This places PfRPN10 as the proteasomal docking site for ubiquitinated-substrate shuttle proteins in P. falciparum.\",\n      \"method\": \"Crystal structure determination of PfDsk2 UBL domain (1.30 Å resolution) combined with binding affinity measurements (dissociation constants) for the PfDsk2–PfRPN10 interaction\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure plus affinity measurements, but single lab and binding interface with PfRPN10 inferred from structural comparison rather than direct mutagenesis of PfRPN10 itself\",\n      \"pmids\": [\"32057831\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In a Xenopus oocyte heterologous model, P. berghei Rpt3 (PbRpt3) was immunoprecipitated with an anti-Xenopus RPN10 antibody, demonstrating that PbRpt3 can be incorporated into the 19S regulatory particle complex that contains RPN10. Importantly, PP1c was NOT co-precipitated in this RPN10-containing complex, indicating that the Rpt3–PP1c interaction occurs outside the proteasome and is not part of the RPN10-associated 19S assembly.\",\n      \"method\": \"Co-immunoprecipitation with anti-Xenopus RPN10 antibody in a Xenopus oocyte heterologous expression system\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP in a heterologous system; the result places RPN10 in a 19S complex with PbRpt3 but only indirectly characterizes RPN10's role; single lab, single method\",\n      \"pmids\": [\"41373862\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"P. falciparum RPN10 (PF3D7_0807800) is a subunit of the 19S regulatory particle of the 26S proteasome that functions as an intrinsic ubiquitin receptor: its second UIM domain (UIM2) directly binds K48- and K63-linked polyubiquitin chains and ubiquitinated substrates in vitro, and it serves as the proteasomal docking site for the substrate-shuttle protein PfDsk2 via interaction with PfDsk2's UBL domain.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"RPN10 (PF3D7_0807800) is a subunit of the 19S regulatory particle of the Plasmodium 26S proteasome that functions as an intrinsic ubiquitin receptor for the degradation machinery [#0]. It carries two ubiquitin-interacting motif (UIM) domains, of which UIM2 is the functional receptor: in vitro, PfUIM2 (alone or in combination with UIM1) binds both K48- and K63-linked polyubiquitin chains and pulls down a broad range of ubiquitin conjugates from parasite extracts, whereas UIM1 alone does not bind [#0]. Beyond direct chain recognition, RPN10 serves as the proteasomal docking site for the substrate-shuttle protein PfDsk2, binding the PfDsk2 UBL domain with an affinity comparable to the human system despite structural differences at the interface [#1]. In a Xenopus oocyte heterologous system, RPN10 is found in a 19S assembly containing P. berghei Rpt3 but lacking PP1c, indicating the Rpt3–PP1c interaction occurs outside the RPN10-associated regulatory particle [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"It was unknown how the plasmodial proteasome recognizes ubiquitinated substrates; this work established RPN10 as the intrinsic ubiquitin receptor and pinpointed UIM2 as the responsible domain.\",\n      \"evidence\": \"Recombinant domain-specific constructs in Ni-NTA pull-down assays with K48/K63 polyubiquitin chains and P. falciparum extracts\",\n      \"pmids\": [\"26639022\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"No structure of the RPN10 UIM–ubiquitin complex\",\n        \"In vitro binding not linked to substrate turnover in intact parasites\",\n        \"Functional distinction between UIM1 and UIM2 in vivo not tested\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Whether Plasmodium uses shuttle factors to deliver substrates to the proteasome was open; this work showed RPN10 is the docking site for the PfDsk2 shuttle protein via its UBL domain.\",\n      \"evidence\": \"1.30 Å crystal structure of PfDsk2 UBL plus dissociation-constant measurements of the PfDsk2–RPN10 interaction\",\n      \"pmids\": [\"32057831\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Binding interface inferred from structural comparison rather than direct RPN10 mutagenesis\",\n        \"No co-structure of the RPN10–PfDsk2 complex\",\n        \"Physiological consequence of the shuttle interaction not tested in parasites\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The composition of the Rpt3-containing 19S particle relative to PP1c was unclear; this work placed RPN10 in a 19S assembly with Rpt3 that excludes PP1c, localizing the Rpt3–PP1c interaction outside the proteasome.\",\n      \"evidence\": \"Co-immunoprecipitation with anti-Xenopus RPN10 antibody in a Xenopus oocyte heterologous expression system (P. berghei Rpt3)\",\n      \"pmids\": [\"41373862\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Single Co-IP in a heterologous system, not validated in Plasmodium\",\n        \"Only indirectly characterizes RPN10's own role\",\n        \"No reciprocal IP or native complex confirmation\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The in vivo requirement of RPN10 for parasite proteasome function, its essentiality, and the cellular consequences of disrupting its ubiquitin-receptor or shuttle-docking activities remain uncharacterized in the available corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"No genetic knockdown/knockout phenotype for RPN10 in Plasmodium\",\n        \"No structural model of RPN10 itself\",\n        \"Contribution of RPN10 to antimalarial proteasome-inhibitor sensitivity unknown\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0043130\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0031593\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0070628\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0008541\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0000502\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0043161\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\n      \"26S proteasome 19S regulatory particle\"\n    ],\n    \"partners\": [\n      \"PfDsk2 (via its UBL domain)\",\n      \"K48- and K63-linked polyubiquitin chains\",\n      \"Rpt3 (in a Xenopus heterologous 19S assembly)\"\n    ],\n    \"other_free_text\": [\n      \"RPN10 contains two UIM domains; UIM2 is the functional ubiquitin-binding domain while UIM1 alone does not bind [#0]\",\n      \"The PfDsk2–RPN10 interface differs structurally from the human homolog yet retains comparable binding affinity [#1]\",\n      \"PP1c is excluded from the RPN10-containing 19S assembly, placing the Rpt3–PP1c interaction outside the proteasome [#2]\"\n    ]\n  }\n}\n```","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0807800","name":null,"product":"26S proteasome regulatory subunit RPN10, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1222900","name":null,"product":"26S proteasome regulatory subunit RPN10, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0110900","name":null,"product":"26S proteasome regulatory subunit RPN10, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RPN10","evaluation":null}