{"gene":"PF3D7_1317800","run_date":"2026-09-08T14:19:06","timeline":{"discoveries":[{"year":2014,"finding":"The cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution places S19 (PF3D7_1317800) as a component of the small (40S) ribosomal subunit; the structure shows emetine binding at the E-site of the small subunit and blocking mRNA/tRNA translocation, establishing the structural context in which S19 resides.","method":"Cryo-EM structure determination at 3.2 Å resolution of the P. falciparum 80S ribosome in complex with emetine","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM structure establishes ribosome architecture including the 40S subunit, but the abstract provides no specific functional or structural detail about S19 itself beyond its membership in the 40S subunit","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"Sub-nanometer cryo-EM reconstructions of blood-stage P. falciparum 80S ribosomes confirm that S19 (PF3D7_1317800) is part of the 40S small subunit; atomic models built by flexible fitting reveal structural and dynamic features of the P. falciparum ribosome that differentiate it from the mammalian ribosome.","method":"Cryo-EM with multiple reconstructions at sub-nanometer resolution and flexible-fitting atomic model building","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — multiple cryo-EM reconstructions with atomic model building, but no specific functional or structural detail about S19 individually is reported in the abstract","pmids":["26432834"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"In situ cryo-electron tomography of actively translating ribosomes inside P. falciparum-infected erythrocytes resolves eight high-resolution structures of the native malarial ribosome; S19 (PF3D7_1317800) is confirmed as a component of the 40S subunit within the cellular context, and the study shows that a Plasmodium-specific translation inhibitor decreases elongation factor-bound ribosomal states and apparently upregulates ribosome biogenesis.","method":"In situ cryo-electron tomography with high-resolution structure determination inside infected erythrocytes","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in situ cryo-ET at high resolution is a rigorous Tier 1 method, but the abstract reports no specific finding about S19 itself beyond its presence in the 40S subunit of the native ribosome","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1317800 (S19) is established solely as a structural component of the P. falciparum 40S ribosomal small subunit, as visualized in multiple cryo-EM and cryo-ET structures of the 80S ribosome; no specific catalytic, binding, or regulatory mechanism unique to S19 itself has been experimentally defined in the available literature."},"narrative":{"mechanistic_narrative":"PF3D7_1317800 (S19) is established solely as a structural component of the small (40S) subunit of the Plasmodium falciparum 80S ribosome, as visualized in high-resolution cryo-EM and in situ cryo-ET structures [PMID:24913268, PMID:40825879]. Its assignment to the 40S subunit was made in the 3.2 Å cryo-EM structure of the P. falciparum 80S ribosome bound to emetine [PMID:24913268], confirmed in sub-nanometer reconstructions of blood-stage ribosomes whose atomic models revealed features distinguishing the malarial ribosome from its mammalian counterpart [PMID:26432834], and further placed within actively translating native ribosomes inside infected erythrocytes by in situ cryo-ET [PMID:40825879]. No catalytic, binding, or regulatory activity unique to S19 itself has been characterized in the available corpus; every finding derives from whole-ribosome structural studies in which S19 is one of many resolved subunit components.","teleology":[{"year":2014,"claim":"Establishing where S19 resides within the malarial translation machinery required a high-resolution ribosome structure; the 80S cryo-EM structure placed S19 as a constituent of the 40S small subunit.","evidence":"Cryo-EM at 3.2 Å of the P. falciparum 80S ribosome in complex with emetine","pmids":["24913268"],"confidence":"Medium","gaps":["No functional or structural role specific to S19 is defined beyond 40S membership","The emetine-binding site characterized is on the small subunit generally, not attributed to S19","No interaction partners or contacts of S19 with rRNA or other proteins are described"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"Whether the malarial 40S differs structurally from the mammalian ribosome was addressed by additional reconstructions that confirmed S19 as a 40S component and revealed parasite-specific ribosome features.","evidence":"Cryo-EM with multiple sub-nanometer reconstructions and flexible-fitting atomic models of blood-stage 80S ribosomes","pmids":["26432834"],"confidence":"Medium","gaps":["Parasite-specific features are attributed to the ribosome as a whole, not to S19 individually","No unique role of S19 in the divergent features is established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Whether S19 assignments from purified-ribosome structures hold in the native cellular context was tested by in situ cryo-ET of translating ribosomes, confirming S19 in the 40S subunit within infected erythrocytes.","evidence":"In situ cryo-electron tomography resolving eight high-resolution states of the native malarial ribosome inside infected erythrocytes","pmids":["40825879"],"confidence":"Medium","gaps":["No S19-specific role in the translation states or ribosome biogenesis response is defined","The inhibitor effect on elongation-factor-bound states is a whole-ribosome observation, not linked to S19"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether S19 possesses any function beyond its structural membership in the 40S subunit — a specific contact, regulatory role, or extraribosomal activity — remains uncharacterized in the available corpus.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No experiment isolates or perturbs S19 specifically","No binding partners, substrates, or regulatory functions of S19 are reported","No genetic or biochemical study of S19 apart from whole-ribosome structures exists in the corpus"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["40S small ribosomal subunit (P. falciparum 80S ribosome)"],"partners":[],"other_free_text":["S19 is only resolved as one component within whole-ribosome cryo-EM/cryo-ET structures; no S19-specific function, contact, or partner is defined in the corpus.","Emetine binding and translation-inhibitor effects reported in these structures are properties of the small subunit or ribosome as a whole, not attributed to S19 itself."]}},"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":969,"usd":0.013947,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5701,"output_tokens":1820,"usd":0.037003,"stage2_stop_reason":"end_turn"},"total_usd":0.05095,"stage1_batch_id":"msgbatch_011BPjN2BL33F8cJXD1r7V7T","stage2_batch_id":"msgbatch_01Qwg6vP7qxkpL6Gsc7tajsb","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 places S19 (PF3D7_1317800) as a component of the small (40S) ribosomal subunit; the structure shows emetine binding at the E-site of the small subunit and blocking mRNA/tRNA translocation, establishing the structural context in which S19 resides.\",\n      \"method\": \"Cryo-EM structure determination at 3.2 Å resolution of the 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 establishes ribosome architecture including the 40S subunit, but the abstract provides no specific functional or structural detail about S19 itself beyond its membership in the 40S subunit\",\n      \"pmids\": [\"24913268\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Sub-nanometer cryo-EM reconstructions of blood-stage P. falciparum 80S ribosomes confirm that S19 (PF3D7_1317800) is part of the 40S small subunit; atomic models built by flexible fitting reveal structural and dynamic features of the P. falciparum ribosome that differentiate it from the mammalian ribosome.\",\n      \"method\": \"Cryo-EM with multiple reconstructions at sub-nanometer resolution and flexible-fitting atomic model building\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — multiple cryo-EM reconstructions with atomic model building, but no specific functional or structural detail about S19 individually is reported in the abstract\",\n      \"pmids\": [\"26432834\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In situ cryo-electron tomography of actively translating ribosomes inside P. falciparum-infected erythrocytes resolves eight high-resolution structures of the native malarial ribosome; S19 (PF3D7_1317800) is confirmed as a component of the 40S subunit within the cellular context, and the study shows that a Plasmodium-specific translation inhibitor decreases elongation factor-bound ribosomal states and apparently upregulates ribosome biogenesis.\",\n      \"method\": \"In situ cryo-electron tomography with high-resolution structure determination inside infected erythrocytes\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in situ cryo-ET at high resolution is a rigorous Tier 1 method, but the abstract reports no specific finding about S19 itself beyond its presence in the 40S subunit of the native ribosome\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1317800 (S19) is established solely as a structural component of the P. falciparum 40S ribosomal small subunit, as visualized in multiple cryo-EM and cryo-ET structures of the 80S ribosome; no specific catalytic, binding, or regulatory mechanism unique to S19 itself has been experimentally defined in the available literature.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1317800 (S19) is established solely as a structural component of the small (40S) subunit of the Plasmodium falciparum 80S ribosome, as visualized in high-resolution cryo-EM and in situ cryo-ET structures [#0, #2]. Its assignment to the 40S subunit was made in the 3.2 Å cryo-EM structure of the P. falciparum 80S ribosome bound to emetine [#0], confirmed in sub-nanometer reconstructions of blood-stage ribosomes whose atomic models revealed features distinguishing the malarial ribosome from its mammalian counterpart [#1], and further placed within actively translating native ribosomes inside infected erythrocytes by in situ cryo-ET [#2]. No catalytic, binding, or regulatory activity unique to S19 itself has been characterized in the available corpus; every finding derives from whole-ribosome structural studies in which S19 is one of many resolved subunit components.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Establishing where S19 resides within the malarial translation machinery required a high-resolution ribosome structure; the 80S cryo-EM structure placed S19 as a constituent of the 40S small subunit.\",\n      \"evidence\": \"Cryo-EM at 3.2 Å of the P. falciparum 80S ribosome in complex with emetine\",\n      \"pmids\": [\"24913268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional or structural role specific to S19 is defined beyond 40S membership\",\n        \"The emetine-binding site characterized is on the small subunit generally, not attributed to S19\",\n        \"No interaction partners or contacts of S19 with rRNA or other proteins are described\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Whether the malarial 40S differs structurally from the mammalian ribosome was addressed by additional reconstructions that confirmed S19 as a 40S component and revealed parasite-specific ribosome features.\",\n      \"evidence\": \"Cryo-EM with multiple sub-nanometer reconstructions and flexible-fitting atomic models of blood-stage 80S ribosomes\",\n      \"pmids\": [\"26432834\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Parasite-specific features are attributed to the ribosome as a whole, not to S19 individually\",\n        \"No unique role of S19 in the divergent features is established\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether S19 assignments from purified-ribosome structures hold in the native cellular context was tested by in situ cryo-ET of translating ribosomes, confirming S19 in the 40S subunit within infected erythrocytes.\",\n      \"evidence\": \"In situ cryo-electron tomography resolving eight high-resolution states of the native malarial ribosome inside infected erythrocytes\",\n      \"pmids\": [\"40825879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No S19-specific role in the translation states or ribosome biogenesis response is defined\",\n        \"The inhibitor effect on elongation-factor-bound states is a whole-ribosome observation, not linked to S19\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether S19 possesses any function beyond its structural membership in the 40S subunit — a specific contact, regulatory role, or extraribosomal activity — remains uncharacterized in the available corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No experiment isolates or perturbs S19 specifically\",\n        \"No binding partners, substrates, or regulatory functions of S19 are reported\",\n        \"No genetic or biochemical study of S19 apart from whole-ribosome structures exists in the corpus\"\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    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006412\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\n      \"40S small ribosomal subunit (P. falciparum 80S ribosome)\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"S19 is only resolved as one component within whole-ribosome cryo-EM/cryo-ET structures; no S19-specific function, contact, or partner is defined in the corpus.\",\n      \"Emetine binding and translation-inhibitor effects reported in these structures are properties of the small subunit or ribosome as a whole, not attributed to S19 itself.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1317800","name":null,"product":"40S ribosomal protein S19","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1416300","name":null,"product":"40S ribosomal protein S19, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1418500","name":null,"product":"40S ribosomal protein S19, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}