{"gene":"PF3D7_0306900","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":2014,"finding":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution revealed the atomic-level organization of the small (40S) subunit, within which S23 (PF3D7_0306900) is a component; the structure showed emetine binding to the E-site of the small subunit and blocking mRNA/tRNA translocation.","method":"Cryo-EM structure determination at 3.2 Å resolution of the native P. falciparum 80S ribosome in complex with emetine","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM structure from a single study; S23 is implicitly present as a 40S component but is not individually characterized or functionally validated in isolation","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"Five cryo-EM reconstructions of the P. falciparum 80S ribosome purified from blood-stage schizonts at sub-nanometer resolution with atomic model building confirmed S23 (PF3D7_0306900) as part of the small ribosomal subunit and revealed structural and dynamic features distinguishing the P. falciparum ribosome from mammalian ribosomes.","method":"Cryo-EM with multiple conformational states resolved; flexible fitting to build atomic models","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — multiple cryo-EM structures from a single study; S23 is a constituent of the resolved small subunit but is not individually functionally interrogated","pmids":["26432834"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"In situ cryo-electron tomography of P. falciparum-infected erythrocytes determined eight high-resolution structures of the native malarial ribosome in actively translating states, establishing the molecular context of the 40S subunit (including S23/PF3D7_0306900) within the translation elongation cycle inside the native cellular environment.","method":"In situ cryo-electron tomography inside P. falciparum-infected human erythrocytes; eight high-resolution ribosome structures in translating states","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in situ cryo-ET with high resolution, single study; S23 is a structural component of the 40S subunit resolved but is not individually dissected","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0306900 (S23) is established as a structural component of the P. falciparum 40S ribosomal small subunit, whose atomic organization has been resolved by cryo-EM and in situ cryo-ET; beyond its membership in the 40S subunit, no specific biochemical activity, binding partner, or individual functional role has been experimentally assigned to S23 itself in the available literature."},"narrative":{"mechanistic_narrative":"PF3D7_0306900 (S23) is a structural component of the small (40S) subunit of the Plasmodium falciparum 80S ribosome, identified within the atomic organization of the small subunit by high-resolution cryo-EM of the native parasite ribosome [PMID:24913268, PMID:26432834]. In situ cryo-electron tomography of P. falciparum-infected erythrocytes has placed the 40S subunit, including S23, within the molecular context of actively translating ribosomes across the elongation cycle in the native cellular environment [PMID:40825879]. Beyond its membership in the 40S small ribosomal subunit as resolved by these structural studies, no specific biochemical activity, individual binding partner, or distinct functional role has been experimentally assigned to S23 itself in the available corpus.","teleology":[{"year":2014,"claim":"The first atomic-resolution view of the P. falciparum ribosome was needed to define the composition and organization of the parasite translation machinery, within which S23 could be placed as a small-subunit constituent.","evidence":"Cryo-EM structure at 3.2 Å of the native P. falciparum 80S ribosome bound to emetine, resolving the 40S subunit","pmids":["24913268"],"confidence":"Medium","gaps":["S23 is present as a 40S component but is not individually characterized or functionally validated","no S23-specific interaction or activity distinguished from the bulk subunit","the emetine E-site drug interaction is a small-subunit property, not an S23-specific one"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"Whether the parasite small subunit carries structural or dynamic features distinguishing it from the mammalian ribosome — a question relevant to selective targeting — was addressed by resolving multiple conformational states.","evidence":"Five cryo-EM reconstructions of the schizont-stage 80S ribosome with flexible atomic model building, confirming S23 in the small subunit","pmids":["26432834"],"confidence":"Medium","gaps":["S23 is a constituent of the resolved subunit but is not individually functionally interrogated","no assignment of an S23-specific role in the observed conformational dynamics"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"To move from purified structures to the native functional context, the ribosome was resolved inside intact infected cells across translating states, establishing where the 40S subunit and S23 sit within the elongation cycle in situ.","evidence":"In situ cryo-electron tomography of P. falciparum-infected human erythrocytes yielding eight high-resolution structures of translating ribosomes","pmids":["40825879"],"confidence":"Medium","gaps":["S23 is resolved as a structural component but is not individually dissected","no mechanistic role for S23 in elongation established beyond subunit membership"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"It remains unknown whether S23 has any function, interaction, or property distinct from its structural membership in the 40S subunit.","evidence":"No experiment in the corpus isolates or perturbs S23 itself","pmids":[],"confidence":"Medium","gaps":["no genetic knockdown/knockout or essentiality data for S23 specifically","no S23-specific binding partner, RNA contact, or biochemical activity defined","no evidence for extraribosomal or moonlighting roles"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["40S small ribosomal subunit of the P. falciparum 80S ribosome"],"partners":[],"other_free_text":["S23 is characterized in the available corpus only as a structural constituent of the 40S small ribosomal subunit; no S23-specific binding partner, activity, or individual functional role has been experimentally assigned.","Structural studies resolve the 40S subunit (including S23) in native, drug-bound (emetine), multiple-conformation, and in situ actively-translating states of the P. falciparum ribosome."]}},"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":941,"usd":0.013737,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5627,"output_tokens":1735,"usd":0.035755,"stage2_stop_reason":"end_turn"},"total_usd":0.049492,"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\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution revealed the atomic-level organization of the small (40S) subunit, within which S23 (PF3D7_0306900) is a component; the structure showed emetine binding to the E-site of the small subunit and blocking mRNA/tRNA translocation.\",\n      \"method\": \"Cryo-EM structure determination at 3.2 Å resolution of the native P. falciparum 80S ribosome in complex with emetine\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM structure from a single study; S23 is implicitly present as a 40S component but is not individually characterized or functionally validated in isolation\",\n      \"pmids\": [\"24913268\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Five cryo-EM reconstructions of the P. falciparum 80S ribosome purified from blood-stage schizonts at sub-nanometer resolution with atomic model building confirmed S23 (PF3D7_0306900) as part of the small ribosomal subunit and revealed structural and dynamic features distinguishing the P. falciparum ribosome from mammalian ribosomes.\",\n      \"method\": \"Cryo-EM with multiple conformational states resolved; flexible fitting to build atomic models\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — multiple cryo-EM structures from a single study; S23 is a constituent of the resolved small subunit but is not individually functionally interrogated\",\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 erythrocytes determined eight high-resolution structures of the native malarial ribosome in actively translating states, establishing the molecular context of the 40S subunit (including S23/PF3D7_0306900) within the translation elongation cycle inside the native cellular environment.\",\n      \"method\": \"In situ cryo-electron tomography inside P. falciparum-infected human erythrocytes; eight high-resolution ribosome structures in translating states\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in situ cryo-ET with high resolution, single study; S23 is a structural component of the 40S subunit resolved but is not individually dissected\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0306900 (S23) is established as a structural component of the P. falciparum 40S ribosomal small subunit, whose atomic organization has been resolved by cryo-EM and in situ cryo-ET; beyond its membership in the 40S subunit, no specific biochemical activity, binding partner, or individual functional role has been experimentally assigned to S23 itself in the available literature.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0306900 (S23) is a structural component of the small (40S) subunit of the Plasmodium falciparum 80S ribosome, identified within the atomic organization of the small subunit by high-resolution cryo-EM of the native parasite ribosome [#0, #1]. In situ cryo-electron tomography of P. falciparum-infected erythrocytes has placed the 40S subunit, including S23, within the molecular context of actively translating ribosomes across the elongation cycle in the native cellular environment [#2]. Beyond its membership in the 40S small ribosomal subunit as resolved by these structural studies, no specific biochemical activity, individual binding partner, or distinct functional role has been experimentally assigned to S23 itself in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"The first atomic-resolution view of the P. falciparum ribosome was needed to define the composition and organization of the parasite translation machinery, within which S23 could be placed as a small-subunit constituent.\",\n      \"evidence\": \"Cryo-EM structure at 3.2 Å of the native P. falciparum 80S ribosome bound to emetine, resolving the 40S subunit\",\n      \"pmids\": [\"24913268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"S23 is present as a 40S component but is not individually characterized or functionally validated\",\n        \"no S23-specific interaction or activity distinguished from the bulk subunit\",\n        \"the emetine E-site drug interaction is a small-subunit property, not an S23-specific one\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Whether the parasite small subunit carries structural or dynamic features distinguishing it from the mammalian ribosome — a question relevant to selective targeting — was addressed by resolving multiple conformational states.\",\n      \"evidence\": \"Five cryo-EM reconstructions of the schizont-stage 80S ribosome with flexible atomic model building, confirming S23 in the small subunit\",\n      \"pmids\": [\"26432834\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"S23 is a constituent of the resolved subunit but is not individually functionally interrogated\",\n        \"no assignment of an S23-specific role in the observed conformational dynamics\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"To move from purified structures to the native functional context, the ribosome was resolved inside intact infected cells across translating states, establishing where the 40S subunit and S23 sit within the elongation cycle in situ.\",\n      \"evidence\": \"In situ cryo-electron tomography of P. falciparum-infected human erythrocytes yielding eight high-resolution structures of translating ribosomes\",\n      \"pmids\": [\"40825879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"S23 is resolved as a structural component but is not individually dissected\",\n        \"no mechanistic role for S23 in elongation established beyond subunit membership\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether S23 has any function, interaction, or property distinct from its structural membership in the 40S subunit.\",\n      \"evidence\": \"No experiment in the corpus isolates or perturbs S23 itself\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"no genetic knockdown/knockout or essentiality data for S23 specifically\",\n        \"no S23-specific binding partner, RNA contact, or biochemical activity defined\",\n        \"no evidence for extraribosomal or moonlighting roles\"\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:0006414\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\n      \"40S small ribosomal subunit of the P. falciparum 80S ribosome\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"S23 is characterized in the available corpus only as a structural constituent of the 40S small ribosomal subunit; no S23-specific binding partner, activity, or individual functional role has been experimentally assigned.\",\n      \"Structural studies resolve the 40S subunit (including S23) in native, drug-bound (emetine), multiple-conformation, and in situ actively-translating states of the P. falciparum ribosome.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0306900","name":null,"product":"40S ribosomal protein S23, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0405300","name":null,"product":"40S ribosomal protein S23, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0835700","name":null,"product":"40S ribosomal protein S23, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}