{"gene":"PF3D7_0931800","run_date":"2026-09-08T12:51:27","timeline":{"discoveries":[{"year":2023,"finding":"A mutation in the P. falciparum 20S proteasome β6 subunit (A117D) confers resistance to the macrocyclic peptide inhibitor TDI-8304, demonstrating that the β6 subunit contributes to the inhibitor-binding site of Pf20S. Cryo-EM structure of Pf20Sβ6A117D with WLW-vs (a tripeptide vinyl sulfone β2 inhibitor) revealed that this β6 mutation causes collateral sensitivity by altering proteasome architecture such that WLW-vs binds β2 and β5 more effectively.","method":"High-resolution cryo-EM structural analysis of Pf20S wild-type and Pf20Sβ6A117D mutant complexes with inhibitors; resistance selection in P. falciparum culture","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure with mutagenesis (A117D) validated by functional resistance and collateral sensitivity assays; single lab but multiple orthogonal methods","pmids":["38097652"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"finding":"The cryo-EM structure of the P. falciparum 20S proteasome bound to the reversible inhibitor SW584 revealed that SW584 binds non-covalently at a pocket at the β5/β6/β3 subunit interface, distinct from the catalytic threonine, exploiting species-selective structural differences between the Pf and human proteasomes. This establishes PF3D7_0931800 (β6 subunit) as a structural component forming the inhibitor-binding interface.","method":"Cryo-EM structure determination of Pf_proteasome–SW584 complex; resistance selection identifying Pfβ5 active-site mutations; His8-tagged β7-facilitated purification","journal":"Cell chemical biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure with functional validation (resistance mutations, inhibition assays); single lab but multiple orthogonal methods","pmids":["39084225"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"finding":"Cryo-EM structure of the P. falciparum 20S proteasome at 3.6 Å resolution revealed the active-site architecture of the complex, including the β2-subunit active site. PF3D7_0931800 (β6) is a structural subunit of the Pf20S complex resolved in this structure, establishing its membership and position within the assembled 20S core.","method":"Cryo-EM single-particle analysis at 3.6 Å; substrate profiling; in vitro inhibitor assays","journal":"Nature","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM structure, but findings specific to β6 (PF3D7_0931800) beyond complex membership are not explicitly detailed in the abstract","pmids":["26863983"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2019,"finding":"Cryo-EM structure of the Pf20S–PfPA28 complex at 3.8–3.9 Å resolution placed PF3D7_0931800 (β6) as a component of the 20S catalytic core that interacts asymmetrically with the PA28 regulator, with PfPA28 strongly engaging subunits on only one side of the core.","method":"Cryo-EM single-particle analysis; crystal structure of PfPA28; SAXS; molecular dynamics simulations; genetic deletion of PA28","journal":"Nature microbiology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM structure establishes β6 as part of the 20S core complex; findings specific to β6 subunit itself are not individually detailed in the abstract","pmids":["31384003"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0931800 (proteasome β6 subunit) is a structural component of the P. falciparum 20S proteasome catalytic core whose active-site region contributes to an inhibitor-binding interface shared with the β5 and β3 subunits; a point mutation in β6 (A117D) confers resistance to the selective macrocyclic inhibitor TDI-8304 while simultaneously causing collateral sensitivity to β2-targeting inhibitors, as revealed by cryo-EM structures of wild-type and mutant complexes."},"narrative":{"mechanistic_narrative":"PF3D7_0931800 encodes the β6 subunit of the Plasmodium falciparum 20S proteasome, a structural component of the assembled catalytic core resolved in cryo-EM structures of the Pf20S complex [PMID:26863983, PMID:31384003]. Within the core, β6 sits at an inhibitor-binding interface shared with the β5 and β3 subunits: the reversible inhibitor SW584 binds non-covalently at a pocket at the β5/β6/β3 interface, distinct from the catalytic threonine, exploiting structural differences between the Pf and human proteasomes [PMID:39084225]. A point mutation in β6 (A117D) confers resistance to the macrocyclic peptide inhibitor TDI-8304, directly establishing that β6 contributes to the Pf20S inhibitor-binding site; the same mutation causes collateral sensitivity by altering proteasome architecture so that the β2 inhibitor WLW-vs binds the β2 and β5 sites more effectively [PMID:38097652]. As a core subunit, β6 also participates in the asymmetric engagement of the Pf20S core by the PfPA28 regulator [PMID:31384003]. Beyond its structural role in the 20S core and its contribution to the shared inhibitor-binding interface, the catalytic or substrate-specific function of β6 itself has not been individually characterized in the available corpus.","teleology":[{"year":2016,"claim":"Establishing the subunit architecture of the P. falciparum 20S proteasome was needed to locate individual catalytic-core subunits; the high-resolution structure placed β6 within the assembled complex.","evidence":"Cryo-EM single-particle analysis of Pf20S at 3.6 Å with substrate profiling and in vitro inhibitor assays","pmids":["26863983"],"confidence":"Medium","gaps":["β6-specific catalytic contribution not resolved beyond complex membership","no functional data on β6 substrate specificity"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2019,"claim":"How the Pf20S core engages its PA28 regulator was unknown; the Pf20S–PfPA28 structure positioned β6 as a core subunit within an asymmetric core–regulator interaction.","evidence":"Cryo-EM of Pf20S–PfPA28 at 3.8–3.9 Å with PfPA28 crystallography, SAXS, MD simulations, and PA28 genetic deletion","pmids":["31384003"],"confidence":"Medium","gaps":["specific role of β6 in PA28 engagement not individually defined","functional consequence of asymmetric regulation for β6 activity unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"claim":"Whether β6 contributes to inhibitor binding was untested; a resistance-conferring β6 A117D mutation demonstrated β6 forms part of the Pf20S inhibitor-binding site and shapes cross-inhibitor sensitivity.","evidence":"Resistance selection in P. falciparum culture plus cryo-EM of wild-type and Pf20Sβ6A117D complexes with the β2 inhibitor WLW-vs","pmids":["38097652"],"confidence":"High","gaps":["mechanism by which A117D remodels the β2/β5 sites for collateral sensitivity not fully resolved","physiological cost of β6 A117D on proteasome function untested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"claim":"Defining a druggable, species-selective pocket required mapping where reversible inhibitors bind; SW584 was shown to bind non-covalently at the β5/β6/β3 interface, confirming β6 as part of a shared inhibitor-binding surface.","evidence":"Cryo-EM of the Pf proteasome–SW584 complex, His8-tagged β7-facilitated purification, and resistance selection identifying Pfβ5 active-site mutations","pmids":["39084225"],"confidence":"High","gaps":["direct β6 contribution to SW584 affinity vs. β5/β3 not deconvoluted","no β6 mutant validation of the SW584 pocket"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The intrinsic catalytic activity, substrate specificity, and non-structural roles of the β6 subunit itself remain undefined in the available corpus.","evidence":"","pmids":[],"confidence":"Medium","gaps":["no β6-specific enzymatic characterization","no assembly or turnover studies isolating β6","role of β6 in parasite viability not directly tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["P. falciparum 20S proteasome catalytic core","Pf20S–PfPA28 complex"],"partners":["Β5 SUBUNIT (INHIBITOR-BINDING INTERFACE)","Β3 SUBUNIT (INHIBITOR-BINDING INTERFACE)","PFPA28 REGULATOR (VIA 20S CORE)"],"other_free_text":["β6 subunit contributes to the shared β5/β6/β3 inhibitor-binding interface of the Pf20S proteasome [#1].","β6 A117D mutation confers resistance to TDI-8304 and collateral sensitivity to the β2 inhibitor WLW-vs [#0].","β6 is a structural subunit resolved within the assembled Pf20S catalytic core [#2, #3].","Catalytic and substrate-specific functions of β6 itself are uncharacterized in the corpus."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"26863983","id":"PMC_26863983","title":"Structure- and function-based design of Plasmodium-selective proteasome inhibitors.","date":"2016","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/26863983","citation_count":196,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24533266","id":"PMC_24533266","title":"The proteasome of malaria parasites: A multi-stage drug target for chemotherapeutic intervention?","date":"2012","source":"International journal for parasitology. Drugs and drug resistance","url":"https://pubmed.ncbi.nlm.nih.gov/24533266","citation_count":64,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"31384003","id":"PMC_31384003","title":"The structure of the PA28-20S proteasome complex from Plasmodium falciparum and implications for proteostasis.","date":"2019","source":"Nature microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/31384003","citation_count":37,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34548400","id":"PMC_34548400","title":"Design of proteasome inhibitors with oral efficacy in vivo against Plasmodium falciparum and selectivity over the human proteasome.","date":"2021","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/34548400","citation_count":33,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38097652","id":"PMC_38097652","title":"Structures revealing mechanisms of resistance and collateral sensitivity of Plasmodium falciparum to proteasome inhibitors.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38097652","citation_count":21,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39084225","id":"PMC_39084225","title":"Identification of potent and reversible piperidine carboxamides that are species-selective orally active proteasome inhibitors to treat malaria.","date":"2024","source":"Cell chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/39084225","citation_count":11,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41148577","id":"PMC_41148577","title":"Optimization of Species-Selective Reversible Proteasome Inhibitors for the Treatment of Malaria.","date":"2025","source":"Journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/41148577","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6131,"output_tokens":1375,"usd":0.019509,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6269,"output_tokens":2146,"usd":0.042498,"stage2_stop_reason":"end_turn"},"total_usd":0.062007,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"A mutation in the P. falciparum 20S proteasome β6 subunit (A117D) confers resistance to the macrocyclic peptide inhibitor TDI-8304, demonstrating that the β6 subunit contributes to the inhibitor-binding site of Pf20S. Cryo-EM structure of Pf20Sβ6A117D with WLW-vs (a tripeptide vinyl sulfone β2 inhibitor) revealed that this β6 mutation causes collateral sensitivity by altering proteasome architecture such that WLW-vs binds β2 and β5 more effectively.\",\n      \"method\": \"High-resolution cryo-EM structural analysis of Pf20S wild-type and Pf20Sβ6A117D mutant complexes with inhibitors; resistance selection in P. falciparum culture\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure with mutagenesis (A117D) validated by functional resistance and collateral sensitivity assays; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"38097652\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The cryo-EM structure of the P. falciparum 20S proteasome bound to the reversible inhibitor SW584 revealed that SW584 binds non-covalently at a pocket at the β5/β6/β3 subunit interface, distinct from the catalytic threonine, exploiting species-selective structural differences between the Pf and human proteasomes. This establishes PF3D7_0931800 (β6 subunit) as a structural component forming the inhibitor-binding interface.\",\n      \"method\": \"Cryo-EM structure determination of Pf_proteasome–SW584 complex; resistance selection identifying Pfβ5 active-site mutations; His8-tagged β7-facilitated purification\",\n      \"journal\": \"Cell chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure with functional validation (resistance mutations, inhibition assays); single lab but multiple orthogonal methods\",\n      \"pmids\": [\"39084225\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Cryo-EM structure of the P. falciparum 20S proteasome at 3.6 Å resolution revealed the active-site architecture of the complex, including the β2-subunit active site. PF3D7_0931800 (β6) is a structural subunit of the Pf20S complex resolved in this structure, establishing its membership and position within the assembled 20S core.\",\n      \"method\": \"Cryo-EM single-particle analysis at 3.6 Å; substrate profiling; in vitro inhibitor assays\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM structure, but findings specific to β6 (PF3D7_0931800) beyond complex membership are not explicitly detailed in the abstract\",\n      \"pmids\": [\"26863983\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Cryo-EM structure of the Pf20S–PfPA28 complex at 3.8–3.9 Å resolution placed PF3D7_0931800 (β6) as a component of the 20S catalytic core that interacts asymmetrically with the PA28 regulator, with PfPA28 strongly engaging subunits on only one side of the core.\",\n      \"method\": \"Cryo-EM single-particle analysis; crystal structure of PfPA28; SAXS; molecular dynamics simulations; genetic deletion of PA28\",\n      \"journal\": \"Nature microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM structure establishes β6 as part of the 20S core complex; findings specific to β6 subunit itself are not individually detailed in the abstract\",\n      \"pmids\": [\"31384003\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0931800 (proteasome β6 subunit) is a structural component of the P. falciparum 20S proteasome catalytic core whose active-site region contributes to an inhibitor-binding interface shared with the β5 and β3 subunits; a point mutation in β6 (A117D) confers resistance to the selective macrocyclic inhibitor TDI-8304 while simultaneously causing collateral sensitivity to β2-targeting inhibitors, as revealed by cryo-EM structures of wild-type and mutant complexes.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0931800 encodes the β6 subunit of the Plasmodium falciparum 20S proteasome, a structural component of the assembled catalytic core resolved in cryo-EM structures of the Pf20S complex [#2, #3]. Within the core, β6 sits at an inhibitor-binding interface shared with the β5 and β3 subunits: the reversible inhibitor SW584 binds non-covalently at a pocket at the β5/β6/β3 interface, distinct from the catalytic threonine, exploiting structural differences between the Pf and human proteasomes [#1]. A point mutation in β6 (A117D) confers resistance to the macrocyclic peptide inhibitor TDI-8304, directly establishing that β6 contributes to the Pf20S inhibitor-binding site; the same mutation causes collateral sensitivity by altering proteasome architecture so that the β2 inhibitor WLW-vs binds the β2 and β5 sites more effectively [#0]. As a core subunit, β6 also participates in the asymmetric engagement of the Pf20S core by the PfPA28 regulator [#3]. Beyond its structural role in the 20S core and its contribution to the shared inhibitor-binding interface, the catalytic or substrate-specific function of β6 itself has not been individually characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Establishing the subunit architecture of the P. falciparum 20S proteasome was needed to locate individual catalytic-core subunits; the high-resolution structure placed β6 within the assembled complex.\",\n      \"evidence\": \"Cryo-EM single-particle analysis of Pf20S at 3.6 Å with substrate profiling and in vitro inhibitor assays\",\n      \"pmids\": [\"26863983\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"β6-specific catalytic contribution not resolved beyond complex membership\", \"no functional data on β6 substrate specificity\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"How the Pf20S core engages its PA28 regulator was unknown; the Pf20S–PfPA28 structure positioned β6 as a core subunit within an asymmetric core–regulator interaction.\",\n      \"evidence\": \"Cryo-EM of Pf20S–PfPA28 at 3.8–3.9 Å with PfPA28 crystallography, SAXS, MD simulations, and PA28 genetic deletion\",\n      \"pmids\": [\"31384003\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"specific role of β6 in PA28 engagement not individually defined\", \"functional consequence of asymmetric regulation for β6 activity unknown\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether β6 contributes to inhibitor binding was untested; a resistance-conferring β6 A117D mutation demonstrated β6 forms part of the Pf20S inhibitor-binding site and shapes cross-inhibitor sensitivity.\",\n      \"evidence\": \"Resistance selection in P. falciparum culture plus cryo-EM of wild-type and Pf20Sβ6A117D complexes with the β2 inhibitor WLW-vs\",\n      \"pmids\": [\"38097652\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"mechanism by which A117D remodels the β2/β5 sites for collateral sensitivity not fully resolved\", \"physiological cost of β6 A117D on proteasome function untested\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defining a druggable, species-selective pocket required mapping where reversible inhibitors bind; SW584 was shown to bind non-covalently at the β5/β6/β3 interface, confirming β6 as part of a shared inhibitor-binding surface.\",\n      \"evidence\": \"Cryo-EM of the Pf proteasome–SW584 complex, His8-tagged β7-facilitated purification, and resistance selection identifying Pfβ5 active-site mutations\",\n      \"pmids\": [\"39084225\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"direct β6 contribution to SW584 affinity vs. β5/β3 not deconvoluted\", \"no β6 mutant validation of the SW584 pocket\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The intrinsic catalytic activity, substrate specificity, and non-structural roles of the β6 subunit itself remain undefined in the available corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"no β6-specific enzymatic characterization\", \"no assembly or turnover studies isolating β6\", \"role of β6 in parasite viability not directly tested\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [\"P. falciparum 20S proteasome catalytic core\", \"Pf20S–PfPA28 complex\"],\n    \"partners\": [\"β5 subunit (inhibitor-binding interface)\", \"β3 subunit (inhibitor-binding interface)\", \"PfPA28 regulator (via 20S core)\"],\n    \"other_free_text\": [\n      \"β6 subunit contributes to the shared β5/β6/β3 inhibitor-binding interface of the Pf20S proteasome [#1].\",\n      \"β6 A117D mutation confers resistance to TDI-8304 and collateral sensitivity to the β2 inhibitor WLW-vs [#0].\",\n      \"β6 is a structural subunit resolved within the assembled Pf20S catalytic core [#2, #3].\",\n      \"Catalytic and substrate-specific functions of β6 itself are uncharacterized in the corpus.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0931800","name":null,"product":"proteasome subunit beta type-6, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0832600","name":null,"product":"proteasome subunit beta type-6, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0730500","name":null,"product":"proteasome subunit beta type-6, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}