{"gene":"PF3D7_0317600","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":2014,"finding":"The cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution revealed that PF3D7_0317600 (40S ribosomal protein S11) is a component of the small ribosomal subunit of the cytoplasmic ribosome. The structure was solved in complex with emetine, establishing the molecular architecture of the small subunit and placing S11 within the 40S particle.","method":"Cryo-EM structure determination at 3.2 Å resolution","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM structure of the whole ribosome establishes S11 as a bona fide component of the 40S subunit, but no functional experiments specific to S11 were performed; membership in the complex is inferred from the structural map","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"Multiple cryo-EM reconstructions of the P. falciparum 80S ribosome purified from blood-stage schizonts at sub-nanometer resolution confirmed that PF3D7_0317600 (S11) is part of the small subunit of the parasite's cytoplasmic ribosome, and atomic models built by flexible fitting captured structural features distinguishing the P. falciparum ribosome from mammalian ribosomes.","method":"Cryo-EM reconstructions (five structures) with atomic model building by flexible fitting","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — multiple cryo-EM reconstructions with atomic model building confirm S11 as a structural component of the 40S subunit, but no experiments directly interrogate S11 function; single group, ribosome-level analysis only","pmids":["26432834"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"In situ cryo-electron tomography of P. falciparum-infected human erythrocytes produced eight high-resolution structures of the native malarial ribosome in actively translating states, confirming PF3D7_0317600 (S11) as a structural component of the small (40S) subunit within the native cellular environment and during active translation elongation.","method":"In situ cryo-electron tomography inside P. falciparum-infected erythrocytes; high-resolution structural determination","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in situ cryo-ET at high resolution in physiological context establishes S11 as part of the actively translating ribosome, but no experiments specifically interrogate S11's individual function; single study","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0317600 (S11) is mechanistically established solely as a structural component of the P. falciparum 40S ribosomal small subunit, as confirmed by multiple cryo-EM and in situ cryo-ET structures of the parasite cytoplasmic ribosome; no S11-specific functional, catalytic, or interaction experiments have been reported."},"narrative":{"mechanistic_narrative":"PF3D7_0317600 (S11) is a structural component of the small (40S) subunit of the P. falciparum cytoplasmic 80S ribosome, established by high-resolution cryo-EM structures of the parasite ribosome [PMID:24913268, PMID:26432834] and confirmed in its native, actively translating state by in situ cryo-electron tomography inside infected erythrocytes [PMID:40825879]. Its placement within the 40S particle was defined structurally, and atomic models built by flexible fitting captured features distinguishing the P. falciparum ribosome from the mammalian ribosome [PMID:26432834]. Beyond its assignment as a 40S component, no S11-specific functional, catalytic, or interaction experiments have been reported in the available corpus; the gene is characterized solely by membership in the small ribosomal subunit.","teleology":[{"year":2014,"claim":"Establishing the molecular architecture of the P. falciparum ribosome answered where S11 sits in the parasite translation machinery, placing it as a bona fide component of the 40S small subunit.","evidence":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å in complex with emetine","pmids":["24913268"],"confidence":"Medium","gaps":["Membership is inferred from the structural map; no functional experiment specific to S11 was performed","No S11-specific interactions or role in subunit assembly defined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"Multiple independent reconstructions from blood-stage schizonts corroborated S11 as a stable structural constituent of the 40S subunit and refined parasite-specific features distinguishing it from the mammalian ribosome.","evidence":"Five cryo-EM reconstructions with atomic model building by flexible fitting of ribosomes purified from schizonts","pmids":["26432834"],"confidence":"Medium","gaps":["Ribosome-level analysis from a single group; no direct interrogation of S11 function","No test of whether parasite-specific features involve S11 directly"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Resolving the native ribosome inside infected erythrocytes confirmed that S11 is a component of the actively translating 40S subunit in its physiological cellular context, not merely in purified preparations.","evidence":"In situ cryo-electron tomography of P. falciparum-infected human erythrocytes yielding eight high-resolution translating-state structures","pmids":["40825879"],"confidence":"Medium","gaps":["Single study; no experiment isolates S11's individual contribution to translation elongation","No functional or genetic assessment of S11 requirement in the parasite"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether S11 has any function beyond structural incorporation into the 40S subunit — including specific rRNA/protein contacts, a role in subunit assembly or translation fidelity, and essentiality in the parasite — remains uncharacterized.","evidence":"No S11-specific functional, genetic, or interaction experiments in the available corpus","pmids":[],"confidence":"Medium","gaps":["No S11 knockout, knockdown, or rescue data","No S11-specific binding partners or contacts defined beyond ribosome membership","No evidence of any extraribosomal role"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["40S small ribosomal subunit of the P. falciparum cytoplasmic 80S ribosome"],"partners":[],"other_free_text":["S11 is established only as a structural component of the 40S subunit; no S11-specific functional, catalytic, or interaction data exist in the corpus.","Atomic models of the P. falciparum ribosome captured features distinguishing it from the mammalian ribosome, but no such distinguishing feature is specifically attributed to S11 [#1].","S11 is present in the actively translating ribosome in the native intraerythrocytic environment [#2]."]}},"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":4453,"output_tokens":976,"usd":0.013999,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5680,"output_tokens":1846,"usd":0.037275,"stage2_stop_reason":"end_turn"},"total_usd":0.051274,"stage1_batch_id":"msgbatch_01DbiymDmubkPpYvdbAu5a7V","stage2_batch_id":"msgbatch_012TbrWvMRH129T7PQ4SmvrJ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"The cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution revealed that PF3D7_0317600 (40S ribosomal protein S11) is a component of the small ribosomal subunit of the cytoplasmic ribosome. The structure was solved in complex with emetine, establishing the molecular architecture of the small subunit and placing S11 within the 40S particle.\",\n      \"method\": \"Cryo-EM structure determination at 3.2 Å resolution\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM structure of the whole ribosome establishes S11 as a bona fide component of the 40S subunit, but no functional experiments specific to S11 were performed; membership in the complex is inferred from the structural map\",\n      \"pmids\": [\"24913268\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Multiple cryo-EM reconstructions of the P. falciparum 80S ribosome purified from blood-stage schizonts at sub-nanometer resolution confirmed that PF3D7_0317600 (S11) is part of the small subunit of the parasite's cytoplasmic ribosome, and atomic models built by flexible fitting captured structural features distinguishing the P. falciparum ribosome from mammalian ribosomes.\",\n      \"method\": \"Cryo-EM reconstructions (five structures) with atomic model building by flexible fitting\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — multiple cryo-EM reconstructions with atomic model building confirm S11 as a structural component of the 40S subunit, but no experiments directly interrogate S11 function; single group, ribosome-level analysis only\",\n      \"pmids\": [\"26432834\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In situ cryo-electron tomography of P. falciparum-infected human erythrocytes produced eight high-resolution structures of the native malarial ribosome in actively translating states, confirming PF3D7_0317600 (S11) as a structural component of the small (40S) subunit within the native cellular environment and during active translation elongation.\",\n      \"method\": \"In situ cryo-electron tomography inside P. falciparum-infected erythrocytes; high-resolution structural determination\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in situ cryo-ET at high resolution in physiological context establishes S11 as part of the actively translating ribosome, but no experiments specifically interrogate S11's individual function; single study\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0317600 (S11) is mechanistically established solely as a structural component of the P. falciparum 40S ribosomal small subunit, as confirmed by multiple cryo-EM and in situ cryo-ET structures of the parasite cytoplasmic ribosome; no S11-specific functional, catalytic, or interaction experiments have been reported.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0317600 (S11) is a structural component of the small (40S) subunit of the P. falciparum cytoplasmic 80S ribosome, established by high-resolution cryo-EM structures of the parasite ribosome [#0, #1] and confirmed in its native, actively translating state by in situ cryo-electron tomography inside infected erythrocytes [#2]. Its placement within the 40S particle was defined structurally, and atomic models built by flexible fitting captured features distinguishing the P. falciparum ribosome from the mammalian ribosome [#1]. Beyond its assignment as a 40S component, no S11-specific functional, catalytic, or interaction experiments have been reported in the available corpus; the gene is characterized solely by membership in the small ribosomal subunit.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Establishing the molecular architecture of the P. falciparum ribosome answered where S11 sits in the parasite translation machinery, placing it as a bona fide component of the 40S small subunit.\",\n      \"evidence\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å in complex with emetine\",\n      \"pmids\": [\"24913268\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Membership is inferred from the structural map; no functional experiment specific to S11 was performed\",\n        \"No S11-specific interactions or role in subunit assembly defined\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Multiple independent reconstructions from blood-stage schizonts corroborated S11 as a stable structural constituent of the 40S subunit and refined parasite-specific features distinguishing it from the mammalian ribosome.\",\n      \"evidence\": \"Five cryo-EM reconstructions with atomic model building by flexible fitting of ribosomes purified from schizonts\",\n      \"pmids\": [\"26432834\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Ribosome-level analysis from a single group; no direct interrogation of S11 function\",\n        \"No test of whether parasite-specific features involve S11 directly\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Resolving the native ribosome inside infected erythrocytes confirmed that S11 is a component of the actively translating 40S subunit in its physiological cellular context, not merely in purified preparations.\",\n      \"evidence\": \"In situ cryo-electron tomography of P. falciparum-infected human erythrocytes yielding eight high-resolution translating-state structures\",\n      \"pmids\": [\"40825879\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Single study; no experiment isolates S11's individual contribution to translation elongation\",\n        \"No functional or genetic assessment of S11 requirement in the parasite\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether S11 has any function beyond structural incorporation into the 40S subunit — including specific rRNA/protein contacts, a role in subunit assembly or translation fidelity, and essentiality in the parasite — remains uncharacterized.\",\n      \"evidence\": \"No S11-specific functional, genetic, or interaction experiments in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"No S11 knockout, knockdown, or rescue data\",\n        \"No S11-specific binding partners or contacts defined beyond ribosome membership\",\n        \"No evidence of any extraribosomal role\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\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      {\"term_id\": \"GO:0005737\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006412\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\n      \"40S small ribosomal subunit of the P. falciparum cytoplasmic 80S ribosome\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"S11 is established only as a structural component of the 40S subunit; no S11-specific functional, catalytic, or interaction data exist in the corpus.\",\n      \"Atomic models of the P. falciparum ribosome captured features distinguishing it from the mammalian ribosome, but no such distinguishing feature is specifically attributed to S11 [#1].\",\n      \"S11 is present in the actively translating ribosome in the native intraerythrocytic environment [#2].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0317600","name":null,"product":"40S ribosomal protein S11, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0807600","name":null,"product":"40S ribosomal protein S11, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0824200","name":null,"product":"40S ribosomal protein S11, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}