{"gene":"PF3D7_1460300","run_date":"2026-09-08T14:19:07","timeline":{"discoveries":[{"year":2014,"finding":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution was solved, revealing RPL29 (PF3D7_1460300) as a component of the 60S large subunit within the assembled cytoplasmic ribosome complex.","method":"Cryo-electron microscopy at 3.2 Å resolution","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM structure of the intact ribosome establishes RPL29 as a structural component, but no functional characterization specific to RPL29 itself is reported beyond complex membership","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"Cryo-EM reconstructions of the P. falciparum 80S ribosome from blood-stage schizonts at sub-nanometer resolution with atomic model building confirmed RPL29 (PF3D7_1460300) as a structural component of the 60S subunit, and revealed structural and dynamic features differentiating P. falciparum ribosomes from mammalian ribosomes.","method":"Cryo-electron microscopy with flexible fitting and atomic model building from purified schizont ribosomes","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — multiple cryo-EM reconstructions with atomic models, but no functional experiment specific to RPL29; complex membership inferred from structural data","pmids":["26432834"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2017,"finding":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å with mefloquine bound confirmed RPL29 (PF3D7_1460300) as a structural component of the assembled 60S ribosomal subunit used in drug-binding studies.","method":"Cryo-electron microscopy at 3.2 Å resolution with mutagenesis of binding residues","journal":"Nature microbiology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM with mutagenesis validation establishes ribosome structure, but no experiment specifically interrogates RPL29 function or binding","pmids":["28288098"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"In situ cryo-electron tomography of P. falciparum-infected erythrocytes at high resolution confirmed RPL29 (PF3D7_1460300) as a component of the native malarial ribosome in actively translating states inside cells, and showed that treatment with a Plasmodium-specific translation inhibitor altered the distribution of elongation factor-bound ribosomal states.","method":"In situ cryo-electron tomography inside infected erythrocytes; drug perturbation experiments","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in situ cryo-ET with drug perturbation is a rigorous method, but no experiment is specific to RPL29; its role is inferred solely from complex membership","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1460300 (RPL29) is established as a structural component of the 60S large subunit of the P. falciparum cytoplasmic 80S ribosome, as confirmed by multiple high-resolution cryo-EM structures; no experiment has yet defined a function or interaction specific to RPL29 beyond its membership in the ribosomal complex."},"narrative":{"mechanistic_narrative":"PF3D7_1460300 (RPL29) is a structural component of the 60S large subunit of the Plasmodium falciparum cytoplasmic 80S ribosome, resolved as part of the assembled complex by high-resolution cryo-EM [PMID:24913268, PMID:26432834]. Its position within the 60S subunit has been confirmed across multiple independent structural datasets, including ribosomes purified from blood-stage schizonts, drug-bound complexes, and native translating ribosomes imaged in situ inside infected erythrocytes [PMID:26432834, PMID:28288098, PMID:40825879]. These structures place RPL29 within a ribosome that displays features distinguishing it from the mammalian ribosome and that serves as a target for Plasmodium-directed translation inhibitors [PMID:26432834, PMID:28288098, PMID:40825879]. No experiment in the available corpus interrogates a function, binding partner, or activity specific to RPL29 beyond its membership in the 60S subunit; its role is inferred solely from being resolved as part of the ribosomal complex.","teleology":[{"year":2014,"claim":"The first question was whether RPL29 is a bona fide constituent of the P. falciparum ribosome; solving the intact 80S structure placed it within the assembled 60S subunit.","evidence":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution","pmids":["24913268"],"confidence":"Medium","gaps":["No functional experiment specific to RPL29; role inferred only from complex membership","No defined interaction network or activity for the protein itself","Contribution of RPL29 to subunit assembly or translation not tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"Building atomic models from schizont-derived ribosomes confirmed RPL29 placement in the 60S subunit and situated it within a ribosome architecture distinct from the mammalian counterpart.","evidence":"Cryo-EM with flexible fitting and atomic model building from purified schizont ribosomes","pmids":["26432834"],"confidence":"Medium","gaps":["Structural presence does not establish any RPL29-specific function","Species-distinguishing features attributed to the whole ribosome, not to RPL29 specifically"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2017,"claim":"Whether the ribosome carrying RPL29 is a viable antimalarial drug target was addressed by resolving a mefloquine-bound 80S structure, again with RPL29 as a confirmed 60S component.","evidence":"Cryo-EM at 3.2 Å with mefloquine bound and mutagenesis of binding residues","pmids":["28288098"],"confidence":"Medium","gaps":["Drug binding and mutagenesis concern other ribosomal sites, not RPL29","No evidence RPL29 participates in drug binding"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Whether RPL29 is part of natively translating ribosomes in the cellular context was established by in situ cryo-ET, which also captured drug-induced shifts in elongation states of the ribosome.","evidence":"In situ cryo-electron tomography inside infected erythrocytes with translation inhibitor perturbation","pmids":["40825879"],"confidence":"Medium","gaps":["Perturbation effects are attributed to the ribosome/elongation factors, not to RPL29","No RPL29-specific role in translation elongation demonstrated"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"No function, binding partner, or activity specific to RPL29 has been defined beyond its structural membership in the 60S subunit.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No genetic knockdown/knockout phenotype for RPL29 characterized","No RPL29-specific interactions or post-translational regulation reported","Any specialized or extraribosomal function remains untested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["60S large ribosomal subunit of the P. falciparum cytoplasmic 80S ribosome"],"partners":[],"other_free_text":["RPL29 is characterized in the available corpus only as a structural component of the P. falciparum 60S ribosomal subunit; no interaction, activity, or phenotype specific to RPL29 has been experimentally defined."]}},"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}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4839,"output_tokens":1123,"usd":0.015681,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5943,"output_tokens":1958,"usd":0.039332,"stage2_stop_reason":"end_turn"},"total_usd":0.055013,"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\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution was solved, revealing RPL29 (PF3D7_1460300) as a component of the 60S large subunit within the assembled cytoplasmic ribosome complex.\",\n      \"method\": \"Cryo-electron microscopy at 3.2 Å resolution\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM structure of the intact ribosome establishes RPL29 as a structural component, but no functional characterization specific to RPL29 itself is reported beyond complex membership\",\n      \"pmids\": [\"24913268\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Cryo-EM reconstructions of the P. falciparum 80S ribosome from blood-stage schizonts at sub-nanometer resolution with atomic model building confirmed RPL29 (PF3D7_1460300) as a structural component of the 60S subunit, and revealed structural and dynamic features differentiating P. falciparum ribosomes from mammalian ribosomes.\",\n      \"method\": \"Cryo-electron microscopy with flexible fitting and atomic model building from purified schizont ribosomes\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — multiple cryo-EM reconstructions with atomic models, but no functional experiment specific to RPL29; complex membership inferred from structural data\",\n      \"pmids\": [\"26432834\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å with mefloquine bound confirmed RPL29 (PF3D7_1460300) as a structural component of the assembled 60S ribosomal subunit used in drug-binding studies.\",\n      \"method\": \"Cryo-electron microscopy at 3.2 Å resolution with mutagenesis of binding residues\",\n      \"journal\": \"Nature microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM with mutagenesis validation establishes ribosome structure, but no experiment specifically interrogates RPL29 function or binding\",\n      \"pmids\": [\"28288098\"],\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 at high resolution confirmed RPL29 (PF3D7_1460300) as a component of the native malarial ribosome in actively translating states inside cells, and showed that treatment with a Plasmodium-specific translation inhibitor altered the distribution of elongation factor-bound ribosomal states.\",\n      \"method\": \"In situ cryo-electron tomography inside infected erythrocytes; drug perturbation experiments\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in situ cryo-ET with drug perturbation is a rigorous method, but no experiment is specific to RPL29; its role is inferred solely from complex membership\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1460300 (RPL29) is established as a structural component of the 60S large subunit of the P. falciparum cytoplasmic 80S ribosome, as confirmed by multiple high-resolution cryo-EM structures; no experiment has yet defined a function or interaction specific to RPL29 beyond its membership in the ribosomal complex.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"PF3D7_1460300 (RPL29) is a structural component of the 60S large subunit of the Plasmodium falciparum cytoplasmic 80S ribosome, resolved as part of the assembled complex by high-resolution cryo-EM [#0, #1]. Its position within the 60S subunit has been confirmed across multiple independent structural datasets, including ribosomes purified from blood-stage schizonts, drug-bound complexes, and native translating ribosomes imaged in situ inside infected erythrocytes [#1, #2, #3]. These structures place RPL29 within a ribosome that displays features distinguishing it from the mammalian ribosome and that serves as a target for Plasmodium-directed translation inhibitors [#1, #2, #3]. No experiment in the available corpus interrogates a function, binding partner, or activity specific to RPL29 beyond its membership in the 60S subunit; its role is inferred solely from being resolved as part of the ribosomal complex.\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"The first question was whether RPL29 is a bona fide constituent of the P. falciparum ribosome; solving the intact 80S structure placed it within the assembled 60S subunit.\",\n      \"evidence\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution\",\n      \"pmids\": [\"24913268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional experiment specific to RPL29; role inferred only from complex membership\",\n        \"No defined interaction network or activity for the protein itself\",\n        \"Contribution of RPL29 to subunit assembly or translation not tested\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Building atomic models from schizont-derived ribosomes confirmed RPL29 placement in the 60S subunit and situated it within a ribosome architecture distinct from the mammalian counterpart.\",\n      \"evidence\": \"Cryo-EM with flexible fitting and atomic model building from purified schizont ribosomes\",\n      \"pmids\": [\"26432834\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Structural presence does not establish any RPL29-specific function\",\n        \"Species-distinguishing features attributed to the whole ribosome, not to RPL29 specifically\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Whether the ribosome carrying RPL29 is a viable antimalarial drug target was addressed by resolving a mefloquine-bound 80S structure, again with RPL29 as a confirmed 60S component.\",\n      \"evidence\": \"Cryo-EM at 3.2 Å with mefloquine bound and mutagenesis of binding residues\",\n      \"pmids\": [\"28288098\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Drug binding and mutagenesis concern other ribosomal sites, not RPL29\",\n        \"No evidence RPL29 participates in drug binding\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether RPL29 is part of natively translating ribosomes in the cellular context was established by in situ cryo-ET, which also captured drug-induced shifts in elongation states of the ribosome.\",\n      \"evidence\": \"In situ cryo-electron tomography inside infected erythrocytes with translation inhibitor perturbation\",\n      \"pmids\": [\"40825879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Perturbation effects are attributed to the ribosome/elongation factors, not to RPL29\",\n        \"No RPL29-specific role in translation elongation demonstrated\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"No function, binding partner, or activity specific to RPL29 has been defined beyond its structural membership in the 60S subunit.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No genetic knockdown/knockout phenotype for RPL29 characterized\",\n        \"No RPL29-specific interactions or post-translational regulation reported\",\n        \"Any specialized or extraribosomal function remains untested\"\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, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0022625\", \"supporting_discovery_ids\": [0, 1, 2, 3]},\n      {\"term_id\": \"GO:0005737\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006412\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\n      \"60S large ribosomal subunit of the P. falciparum cytoplasmic 80S ribosome\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"RPL29 is characterized in the available corpus only as a structural component of the P. falciparum 60S ribosomal subunit; no interaction, activity, or phenotype specific to RPL29 has been experimentally defined.\"\n    ]\n  }\n}\n```","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1460300","name":null,"product":"60S ribosomal protein L29, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1324000","name":null,"product":"60S ribosomal protein L29, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1221400","name":null,"product":"60S ribosomal protein L29, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RPL29","evaluation":null}