{"gene":"PF3D7_1027800","run_date":"2026-09-08T12:51:28","timeline":{"discoveries":[{"year":2014,"finding":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution resolved RPL3 (60S ribosomal protein L3) as a structural component of the large (60S) subunit. The structure placed RPL3 within the ribosomal large subunit architecture, establishing its membership in the native P. falciparum cytoplasmic ribosome complex.","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, but RPL3's role is described only as a structural constituent of the 60S subunit with no specific functional characterization of RPL3 itself beyond complex membership","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"In situ cryo-electron tomography of P. falciparum-infected erythrocytes resolved eight high-resolution structures of the native malarial ribosome in actively translating states; RPL3 is present as a structural component of the large subunit in these native translation-elongation complexes captured inside the cell.","method":"In situ cryo-electron tomography inside P. falciparum-infected human erythrocytes; atomic-resolution structural modelling","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution in-cell structural data, but no specific functional experiment directed at RPL3 itself; RPL3 role inferred from its presence in the solved large-subunit models","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1027800 (RPL3) is established as a structural constituent of the large (60S) subunit of the P. falciparum cytoplasmic 80S ribosome, as visualised in multiple high-resolution cryo-EM and cryo-ET structures; no additional mechanistic role specific to RPL3 (e.g., enzymatic activity, post-translational modification, or defined functional interaction partner) has been experimentally characterised in the available literature."},"narrative":{"mechanistic_narrative":"PF3D7_1027800 (RPL3) is a structural constituent of the large (60S) subunit of the Plasmodium falciparum cytoplasmic 80S ribosome, resolved within the large-subunit architecture by cryo-EM of the intact ribosome and confirmed in native, actively translating elongation complexes imaged in situ by cryo-electron tomography inside infected erythrocytes [PMID:24913268, PMID:40825879]. Beyond its membership in the 60S subunit as a component of the native translational machinery, no mechanistic role specific to RPL3 — enzymatic activity, post-translational modification, or a defined functional interaction partner — has been characterized in the available corpus.","teleology":[{"year":2014,"claim":"Whether RPL3 is a bona fide constituent of the P. falciparum ribosome and where it sits was unknown until the intact 80S ribosome was resolved at near-atomic detail, placing RPL3 within the 60S subunit architecture.","evidence":"Cryo-EM structure of the P. falciparum 80S ribosome bound to emetine at 3.2 Å resolution","pmids":["24913268"],"confidence":"Medium","gaps":["No functional experiment directed at RPL3 itself; role inferred solely from structural placement","No enzymatic activity, modification, or specific partner beyond the ribosome defined","Structure captured with a drug-bound ribosome, not a functional assay of RPL3"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Whether RPL3 occupies the same structural position in ribosomes that are actively translating within the parasite was addressed by imaging native ribosomes in situ, confirming RPL3 as a large-subunit component of elongation-state complexes inside the cell.","evidence":"In situ cryo-electron tomography with atomic-resolution modelling of native ribosomes inside P. falciparum-infected human erythrocytes","pmids":["40825879"],"confidence":"Medium","gaps":["RPL3 role inferred from its presence in solved large-subunit models, not from an RPL3-directed experiment","No mechanistic contribution of RPL3 to translation elongation demonstrated","No RPL3-specific interactions distinguished from bulk ribosome architecture"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether RPL3 has any function beyond structural membership in the 60S subunit — a distinct enzymatic activity, regulatory role, post-translational modification, or specific non-ribosomal partner — remains uncharacterized in the available corpus.","evidence":"No discovery in the timeline addresses RPL3-specific function outside the ribosome complex","pmids":[],"confidence":"Medium","gaps":["No functional or genetic assay targeting RPL3 in P. falciparum","No defined interaction partner specific to RPL3","No evidence for post-translational modification or regulatory activity of RPL3"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["P. falciparum cytoplasmic 80S ribosome (large 60S subunit)"],"partners":[],"other_free_text":["RPL3 is established only as a structural constituent of the 60S large ribosomal subunit; no RPL3-specific function beyond complex membership has been experimentally characterized in the available corpus.","Resolved both in the isolated 80S ribosome (drug-bound) [#0] and in native, actively translating elongation-state ribosomes imaged in situ [#1]."]}},"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":276,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"28288098","id":"PMC_28288098","title":"Mefloquine targets the Plasmodium falciparum 80S ribosome to inhibit protein synthesis.","date":"2017","source":"Nature microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/28288098","citation_count":138,"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":46,"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":10,"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":4,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34252120","id":"PMC_34252120","title":"Screening of viral-vectored P. falciparum pre-erythrocytic candidate vaccine antigens using chimeric rodent parasites.","date":"2021","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/34252120","citation_count":2,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RPL3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5321,"output_tokens":686,"usd":0.013126,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5294,"output_tokens":1581,"usd":0.032997,"stage2_stop_reason":"end_turn"},"total_usd":0.046123,"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\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution resolved RPL3 (60S ribosomal protein L3) as a structural component of the large (60S) subunit. The structure placed RPL3 within the ribosomal large subunit architecture, establishing its membership in the native P. falciparum cytoplasmic ribosome complex.\",\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, but RPL3's role is described only as a structural constituent of the 60S subunit with no specific functional characterization of RPL3 itself beyond complex membership\",\n      \"pmids\": [\"24913268\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In situ cryo-electron tomography of P. falciparum-infected erythrocytes resolved eight high-resolution structures of the native malarial ribosome in actively translating states; RPL3 is present as a structural component of the large subunit in these native translation-elongation complexes captured inside the cell.\",\n      \"method\": \"In situ cryo-electron tomography inside P. falciparum-infected human erythrocytes; atomic-resolution structural modelling\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution in-cell structural data, but no specific functional experiment directed at RPL3 itself; RPL3 role inferred from its presence in the solved large-subunit models\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1027800 (RPL3) is established as a structural constituent of the large (60S) subunit of the P. falciparum cytoplasmic 80S ribosome, as visualised in multiple high-resolution cryo-EM and cryo-ET structures; no additional mechanistic role specific to RPL3 (e.g., enzymatic activity, post-translational modification, or defined functional interaction partner) has been experimentally characterised in the available literature.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1027800 (RPL3) is a structural constituent of the large (60S) subunit of the Plasmodium falciparum cytoplasmic 80S ribosome, resolved within the large-subunit architecture by cryo-EM of the intact ribosome and confirmed in native, actively translating elongation complexes imaged in situ by cryo-electron tomography inside infected erythrocytes [#0, #1]. Beyond its membership in the 60S subunit as a component of the native translational machinery, no mechanistic role specific to RPL3 — enzymatic activity, post-translational modification, or a defined functional interaction partner — has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Whether RPL3 is a bona fide constituent of the P. falciparum ribosome and where it sits was unknown until the intact 80S ribosome was resolved at near-atomic detail, placing RPL3 within the 60S subunit architecture.\",\n      \"evidence\": \"Cryo-EM structure of the P. falciparum 80S ribosome bound to emetine at 3.2 Å resolution\",\n      \"pmids\": [\"24913268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional experiment directed at RPL3 itself; role inferred solely from structural placement\",\n        \"No enzymatic activity, modification, or specific partner beyond the ribosome defined\",\n        \"Structure captured with a drug-bound ribosome, not a functional assay of RPL3\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether RPL3 occupies the same structural position in ribosomes that are actively translating within the parasite was addressed by imaging native ribosomes in situ, confirming RPL3 as a large-subunit component of elongation-state complexes inside the cell.\",\n      \"evidence\": \"In situ cryo-electron tomography with atomic-resolution modelling of native ribosomes inside P. falciparum-infected human erythrocytes\",\n      \"pmids\": [\"40825879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"RPL3 role inferred from its presence in solved large-subunit models, not from an RPL3-directed experiment\",\n        \"No mechanistic contribution of RPL3 to translation elongation demonstrated\",\n        \"No RPL3-specific interactions distinguished from bulk ribosome architecture\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether RPL3 has any function beyond structural membership in the 60S subunit — a distinct enzymatic activity, regulatory role, post-translational modification, or specific non-ribosomal partner — remains uncharacterized in the available corpus.\",\n      \"evidence\": \"No discovery in the timeline addresses RPL3-specific function outside the ribosome complex\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional or genetic assay targeting RPL3 in P. falciparum\",\n        \"No defined interaction partner specific to RPL3\",\n        \"No evidence for post-translational modification or regulatory activity of RPL3\"\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]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0022625\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005737\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006412\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [\n      \"P. falciparum cytoplasmic 80S ribosome (large 60S subunit)\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"RPL3 is established only as a structural constituent of the 60S large ribosomal subunit; no RPL3-specific function beyond complex membership has been experimentally characterized in the available corpus.\",\n      \"Resolved both in the isolated 80S ribosome (drug-bound) [#0] and in native, actively translating elongation-state ribosomes imaged in situ [#1].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1027800","name":null,"product":"60S ribosomal protein L3","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0511900","name":null,"product":"60S ribosomal protein L3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0612200","name":null,"product":"60S ribosomal protein L3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RPL3","evaluation":null}