{"gene":"PF3D7_1003500","run_date":"2026-09-08T12:51:27","timeline":{"discoveries":[{"year":2014,"finding":"PF3D7_1003500 (S20e / 40S ribosomal protein S20e) was resolved as a component of the P. falciparum 80S ribosome small subunit in a cryo-EM structure at 3.2 Å resolution; the structure placed the small subunit E-site as the binding site for emetine, which blocks mRNA/tRNA translocation.","method":"Cryo-EM structure determination at 3.2 Å resolution of the P. falciparum 80S ribosome–emetine complex","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM structure establishes ribosome composition including S20e, but S20e itself is not functionally interrogated beyond its presence in the complex; single study","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"PF3D7_1003500 (S20e) was confirmed as a structural component of the P. falciparum 80S ribosome small subunit through five cryo-EM reconstructions of ribosomes purified from blood-stage schizonts at sub-nanometer resolution, with atomic models built by flexible fitting.","method":"Cryo-EM reconstructions (sub-nanometer resolution) with flexible-fitting atomic model building","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — multiple cryo-EM reconstructions establish S20e as part of the native ribosome structure, but no functional interrogation of S20e specifically; single lab","pmids":["26432834"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"PF3D7_1003500 (S20e) was visualized as part of the native P. falciparum 80S ribosome in eight high-resolution in situ cryo-electron tomography structures of actively translating ribosomes inside infected human erythrocytes; drug-induced perturbation with a Plasmodium-specific translation inhibitor revealed changes in elongation factor-bound ribosomal states and apparent upregulation of ribosome biogenesis.","method":"In situ cryo-electron tomography at high resolution within P. falciparum-infected erythrocytes; integrated structural biology approach","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution in situ cryo-ET establishes S20e as part of the native translating ribosome in cellular context, but S20e is not specifically functionally interrogated; single study","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1003500 (S20e, 40S ribosomal protein S20e) is established solely as a structural component of the P. falciparum 80S ribosome small subunit, as confirmed by multiple cryo-EM and in situ cryo-ET structural studies; no specific enzymatic activity, binding partners, or direct functional role beyond ribosome membership has been experimentally demonstrated for S20e itself."},"narrative":{"mechanistic_narrative":"PF3D7_1003500 (S20e) is established solely as a structural component of the small (40S) subunit of the Plasmodium falciparum 80S ribosome, resolved within high-resolution cryo-EM structures of the intact ribosome [PMID:24913268, PMID:26432834] and visualized in situ as part of natively translating ribosomes inside infected human erythrocytes [PMID:40825879]. No enzymatic activity, specific binding partner, or functional role for S20e beyond its incorporation into the ribosome has been characterized in the available corpus; the studies that place S20e in the small subunit interrogate ribosome-level features—such as the emetine binding site at the small-subunit E-site that blocks mRNA/tRNA translocation [PMID:24913268] and drug-induced shifts in elongation-factor-bound states [PMID:40825879]—rather than S20e itself. Beyond its membership in the 40S subunit, S20e has not been individually functionally dissected in the available corpus.","teleology":[{"year":2014,"claim":"Establishing the molecular composition of the P. falciparum small ribosomal subunit required a high-resolution structure; resolving S20e as a subunit component defined it as part of the parasite translation machinery and situated it near the emetine/E-site translocation region.","evidence":"Cryo-EM structure of the P. falciparum 80S ribosome-emetine complex at 3.2 A","pmids":["24913268"],"confidence":"Medium","gaps":["S20e is placed structurally but not functionally interrogated","No test of whether S20e itself contributes to emetine binding or translocation","No binding partners or activity assigned to S20e"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"Confirming S20e as a bona fide component of the native ribosome (not a preparation artifact) required independent reconstructions from parasite-derived material, reinforcing its assignment to the small subunit.","evidence":"Five cryo-EM reconstructions of ribosomes purified from blood-stage schizonts with flexible-fitting atomic models","pmids":["26432834"],"confidence":"Medium","gaps":["No functional role for S20e distinguished from bulk ribosome","No stage-specific or condition-specific role tested for S20e","Single lab"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Whether S20e is part of ribosomes actively translating in the cellular context was addressed by in situ imaging, confirming its presence in native translating ribosomes and linking the ribosome to drug-responsive translational states.","evidence":"In situ cryo-electron tomography of translating ribosomes inside P. falciparum-infected erythrocytes with a Plasmodium-specific translation inhibitor","pmids":["40825879"],"confidence":"Medium","gaps":["Drug-induced changes are ribosome-level, not attributed to S20e specifically","No S20e-specific perturbation or knockdown","No interaction partners beyond the ribosome assigned to S20e"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether S20e has any function beyond serving as a structural subunit—any regulatory, extra-ribosomal, or drug-target role—remains unaddressed.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No genetic perturbation of S20e reported","No S20e-specific binding partners or post-translational modifications characterized","No evidence of function outside the ribosome"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["P. falciparum 80S ribosome, small (40S) subunit"],"partners":[],"other_free_text":["S20e is documented only as a structural constituent of the P. falciparum 40S ribosomal subunit; no S20e-specific activity, partner, or phenotype has been experimentally demonstrated in the available corpus.","Ribosome-level observations (emetine E-site binding blocking translocation [#0]; drug-induced shifts in elongation-factor states [#2]) pertain to the ribosome, not to S20e individually."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"24913268","id":"PMC_24913268","title":"Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine.","date":"2014","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/24913268","citation_count":272,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26432834","id":"PMC_26432834","title":"Dynamical features of the Plasmodium falciparum ribosome during translation.","date":"2015","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/26432834","citation_count":45,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40825879","id":"PMC_40825879","title":"Integrated structural biology of the native malarial translation machinery and its inhibition by an antimalarial drug.","date":"2025","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/40825879","citation_count":7,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40480224","id":"PMC_40480224","title":"Antimalarial drug artemisinin stabilizes PfRACK1 binding to the ribosome.","date":"2025","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/40480224","citation_count":3,"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":4455,"output_tokens":951,"usd":0.013815,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5675,"output_tokens":1772,"usd":0.036338,"stage2_stop_reason":"end_turn"},"total_usd":0.050153,"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\": 2014,\n      \"finding\": \"PF3D7_1003500 (S20e / 40S ribosomal protein S20e) was resolved as a component of the P. falciparum 80S ribosome small subunit in a cryo-EM structure at 3.2 Å resolution; the structure placed the small subunit E-site as the binding site for emetine, which blocks mRNA/tRNA translocation.\",\n      \"method\": \"Cryo-EM structure determination at 3.2 Å resolution of the P. falciparum 80S ribosome–emetine complex\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM structure establishes ribosome composition including S20e, but S20e itself is not functionally interrogated beyond its presence in the complex; single study\",\n      \"pmids\": [\"24913268\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"PF3D7_1003500 (S20e) was confirmed as a structural component of the P. falciparum 80S ribosome small subunit through five cryo-EM reconstructions of ribosomes purified from blood-stage schizonts at sub-nanometer resolution, with atomic models built by flexible fitting.\",\n      \"method\": \"Cryo-EM reconstructions (sub-nanometer resolution) with flexible-fitting atomic model building\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — multiple cryo-EM reconstructions establish S20e as part of the native ribosome structure, but no functional interrogation of S20e specifically; single lab\",\n      \"pmids\": [\"26432834\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PF3D7_1003500 (S20e) was visualized as part of the native P. falciparum 80S ribosome in eight high-resolution in situ cryo-electron tomography structures of actively translating ribosomes inside infected human erythrocytes; drug-induced perturbation with a Plasmodium-specific translation inhibitor revealed changes in elongation factor-bound ribosomal states and apparent upregulation of ribosome biogenesis.\",\n      \"method\": \"In situ cryo-electron tomography at high resolution within P. falciparum-infected erythrocytes; integrated structural biology approach\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution in situ cryo-ET establishes S20e as part of the native translating ribosome in cellular context, but S20e is not specifically functionally interrogated; single study\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1003500 (S20e, 40S ribosomal protein S20e) is established solely as a structural component of the P. falciparum 80S ribosome small subunit, as confirmed by multiple cryo-EM and in situ cryo-ET structural studies; no specific enzymatic activity, binding partners, or direct functional role beyond ribosome membership has been experimentally demonstrated for S20e itself.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1003500 (S20e) is established solely as a structural component of the small (40S) subunit of the Plasmodium falciparum 80S ribosome, resolved within high-resolution cryo-EM structures of the intact ribosome [#0, #1] and visualized in situ as part of natively translating ribosomes inside infected human erythrocytes [#2]. No enzymatic activity, specific binding partner, or functional role for S20e beyond its incorporation into the ribosome has been characterized in the available corpus; the studies that place S20e in the small subunit interrogate ribosome-level features—such as the emetine binding site at the small-subunit E-site that blocks mRNA/tRNA translocation [#0] and drug-induced shifts in elongation-factor-bound states [#2]—rather than S20e itself. Beyond its membership in the 40S subunit, S20e has not been individually functionally dissected in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Establishing the molecular composition of the P. falciparum small ribosomal subunit required a high-resolution structure; resolving S20e as a subunit component defined it as part of the parasite translation machinery and situated it near the emetine/E-site translocation region.\",\n      \"evidence\": \"Cryo-EM structure of the P. falciparum 80S ribosome-emetine complex at 3.2 A\",\n      \"pmids\": [\"24913268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"S20e is placed structurally but not functionally interrogated\",\n        \"No test of whether S20e itself contributes to emetine binding or translocation\",\n        \"No binding partners or activity assigned to S20e\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Confirming S20e as a bona fide component of the native ribosome (not a preparation artifact) required independent reconstructions from parasite-derived material, reinforcing its assignment to the small subunit.\",\n      \"evidence\": \"Five cryo-EM reconstructions of ribosomes purified from blood-stage schizonts with flexible-fitting atomic models\",\n      \"pmids\": [\"26432834\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional role for S20e distinguished from bulk ribosome\",\n        \"No stage-specific or condition-specific role tested for S20e\",\n        \"Single lab\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether S20e is part of ribosomes actively translating in the cellular context was addressed by in situ imaging, confirming its presence in native translating ribosomes and linking the ribosome to drug-responsive translational states.\",\n      \"evidence\": \"In situ cryo-electron tomography of translating ribosomes inside P. falciparum-infected erythrocytes with a Plasmodium-specific translation inhibitor\",\n      \"pmids\": [\"40825879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Drug-induced changes are ribosome-level, not attributed to S20e specifically\",\n        \"No S20e-specific perturbation or knockdown\",\n        \"No interaction partners beyond the ribosome assigned to S20e\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether S20e has any function beyond serving as a structural subunit—any regulatory, extra-ribosomal, or drug-target role—remains unaddressed.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No genetic perturbation of S20e reported\",\n        \"No S20e-specific binding partners or post-translational modifications characterized\",\n        \"No evidence of function outside the ribosome\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003735\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0022627\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006412\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"complexes\": [\n      \"P. falciparum 80S ribosome, small (40S) subunit\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"S20e is documented only as a structural constituent of the P. falciparum 40S ribosomal subunit; no S20e-specific activity, partner, or phenotype has been experimentally demonstrated in the available corpus.\",\n      \"Ribosome-level observations (emetine E-site binding blocking translocation [#0]; drug-induced shifts in elongation-factor states [#2]) pertain to the ribosome, not to S20e individually.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1003500","name":null,"product":"40S ribosomal protein S20e, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1201900","name":null,"product":"40S ribosomal protein S20e, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0802300","name":null,"product":"40S ribosomal protein S20e, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}