{"gene":"PF3D7_0503800","run_date":"2026-09-07T10:55:52","timeline":{"discoveries":[{"year":2014,"finding":"RPL31 (PF3D7_0503800) was resolved as a structural component of the P. falciparum 80S ribosome in a cryo-EM structure determined at 3.2 Å resolution. The structure placed RPL31 within the 60S large subunit of the cytoplasmic ribosome; the overall structure also revealed how emetine binds the E-site of the small subunit to block mRNA/tRNA translocation.","method":"Cryo-EM structure determination at 3.2 Å resolution of the P. falciparum 80S ribosome","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM structure (Tier 1 method) but the abstract does not describe any specific functional experiment directed at RPL31 itself; structural membership in the complex is inferred from the ribosome assembly, single study","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"RPL31 (PF3D7_0503800) was identified as a component of the P. falciparum 80S ribosome large subunit through cryo-EM reconstructions of ribosomes purified from blood-stage schizonts, with atomic models built by flexible fitting into five sub-nanometer density maps capturing multiple translational states.","method":"Cryo-EM reconstruction (sub-nanometer resolution) of ribosomes purified from P. falciparum blood-stage schizonts; flexible fitting of atomic models","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — rigorous cryo-EM methodology with atomic model building (Tier 1), but no functional experiment specific to RPL31; single study","pmids":["26432834"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2017,"finding":"RPL31 (PF3D7_0503800) was resolved as part of the P. falciparum 80S ribosome large subunit in a 3.2 Å cryo-EM structure obtained with mefloquine bound; the structure enabled mutagenesis of mefloquine-binding residues confirming the ribosome as mefloquine's target, but no specific functional role for RPL31 itself was reported beyond its structural presence.","method":"Cryo-EM structure at 3.2 Å of the P. falciparum 80S ribosome with mefloquine; site-directed mutagenesis of binding-site residues","journal":"Nature microbiology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM plus functional mutagenesis (Tier 1), but experiments were directed at the mefloquine binding site, not RPL31 specifically; structural membership inferred; single study","pmids":["28288098"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"RPL31 (PF3D7_0503800) was visualized as a component of the native P. falciparum 80S ribosome in actively translating states inside infected human erythrocytes, as determined by in situ cryo-electron tomography at high resolution. Eight structures of the ribosome in elongation states were obtained, revealing molecular details of the malarial translation elongation cycle; no specific functional experiment on RPL31 itself was reported beyond its structural membership.","method":"In situ cryo-electron tomography of P. falciparum-infected human erythrocytes; eight high-resolution ribosome structures in actively translating states","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in situ cryo-ET at high resolution in native cellular context (Tier 1), but no experiment specifically targeting RPL31; single study","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0503800 (RPL31) is established solely as a structural component of the 60S large subunit of the P. falciparum cytoplasmic 80S ribosome, as visualized by multiple high-resolution cryo-EM and in situ cryo-ET studies; no specific enzymatic activity, binding partner, post-translational modification, or functional role distinct from its ribosome membership has been experimentally defined for this protein."},"narrative":{"mechanistic_narrative":"PF3D7_0503800 (RPL31) is established as a structural component of the 60S large subunit of the Plasmodium falciparum cytoplasmic 80S ribosome, resolved within the assembled ribosome by high-resolution cryo-EM and, in native infected erythrocytes, by in situ cryo-electron tomography of actively translating ribosomes [PMID:24913268, PMID:40825879]. Its placement in the large subunit has been reproduced across multiple structural studies of blood-stage ribosomes captured in distinct translational and elongation states [PMID:26432834, PMID:40825879], and within structures used to define the ribosomal binding sites of the antimalarials emetine and mefloquine [PMID:24913268, PMID:28288098]. Beyond this membership in the 60S subunit, no enzymatic activity, specific binding partner, post-translational modification, or functional role distinct from its structural role in the ribosome has been characterized for PF3D7_0503800 in the available corpus.","teleology":[{"year":2014,"claim":"Establishing the molecular composition of the P. falciparum ribosome required resolving individual proteins in the assembled complex; RPL31 was placed within the 60S large subunit of the cytoplasmic 80S ribosome.","evidence":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution","pmids":["24913268"],"confidence":"Medium","gaps":["No functional experiment directed at RPL31 itself","Structural membership inferred from ribosome assembly, not from RPL31-specific perturbation"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"Whether RPL31's large-subunit placement holds across ribosomes in different translational states was addressed by reconstructing ribosomes purified from blood-stage schizonts in multiple states.","evidence":"Cryo-EM reconstruction (sub-nanometer) of schizont ribosomes with flexible fitting of atomic models into five density maps","pmids":["26432834"],"confidence":"Medium","gaps":["No functional role assigned to RPL31","No perturbation of RPL31 to test its contribution to translation"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2017,"claim":"Structures used to define antimalarial binding sites reconfirmed RPL31 as a large-subunit component, though the functional mutagenesis targeted the mefloquine site rather than RPL31.","evidence":"Cryo-EM structure at 3.2 Å of the 80S ribosome with mefloquine plus site-directed mutagenesis of binding-site residues","pmids":["28288098"],"confidence":"Medium","gaps":["Mutagenesis addressed the mefloquine site, not RPL31","No evidence RPL31 contacts or contributes to drug binding"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Whether RPL31 is a component of native, actively translating ribosomes in the cellular context was addressed by visualizing ribosomes in situ inside infected human erythrocytes.","evidence":"In situ cryo-electron tomography of P. falciparum-infected erythrocytes yielding eight ribosome structures in elongation states","pmids":["40825879"],"confidence":"Medium","gaps":["No experiment specifically targeting RPL31","Functional contribution of RPL31 to the elongation cycle not tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"It remains unknown whether PF3D7_0503800 has any function, binding partner, or property distinct from its structural membership in the 60S subunit.","evidence":"No RPL31-directed functional, genetic, or biochemical experiment exists in the available corpus","pmids":[],"confidence":"Medium","gaps":["No genetic knockout or knockdown of RPL31","No RPL31-specific binding partners or post-translational modifications identified","No role distinct from ribosome membership defined"],"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":["RPL31 (PF3D7_0503800) is characterized in the available corpus only as a structural component of the 60S large subunit; no binding partner, enzymatic activity, or function distinct from ribosome membership has been experimentally defined.","Structural studies resolving RPL31 also defined the ribosomal binding sites of the antimalarials emetine (E-site, small subunit) [#0] and mefloquine [#2], but no evidence links RPL31 itself to drug binding."]}},"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":4836,"output_tokens":1320,"usd":0.017154,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6160,"output_tokens":2009,"usd":0.040512,"stage2_stop_reason":"end_turn"},"total_usd":0.057666,"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\": \"RPL31 (PF3D7_0503800) was resolved as a structural component of the P. falciparum 80S ribosome in a cryo-EM structure determined at 3.2 Å resolution. The structure placed RPL31 within the 60S large subunit of the cytoplasmic ribosome; the overall structure also revealed how emetine binds the E-site of the small subunit to block mRNA/tRNA translocation.\",\n      \"method\": \"Cryo-EM structure determination at 3.2 Å resolution of the P. falciparum 80S ribosome\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM structure (Tier 1 method) but the abstract does not describe any specific functional experiment directed at RPL31 itself; structural membership in the complex is inferred from the ribosome assembly, single study\",\n      \"pmids\": [\"24913268\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"RPL31 (PF3D7_0503800) was identified as a component of the P. falciparum 80S ribosome large subunit through cryo-EM reconstructions of ribosomes purified from blood-stage schizonts, with atomic models built by flexible fitting into five sub-nanometer density maps capturing multiple translational states.\",\n      \"method\": \"Cryo-EM reconstruction (sub-nanometer resolution) of ribosomes purified from P. falciparum blood-stage schizonts; flexible fitting of atomic models\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — rigorous cryo-EM methodology with atomic model building (Tier 1), but no functional experiment specific to RPL31; single study\",\n      \"pmids\": [\"26432834\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"RPL31 (PF3D7_0503800) was resolved as part of the P. falciparum 80S ribosome large subunit in a 3.2 Å cryo-EM structure obtained with mefloquine bound; the structure enabled mutagenesis of mefloquine-binding residues confirming the ribosome as mefloquine's target, but no specific functional role for RPL31 itself was reported beyond its structural presence.\",\n      \"method\": \"Cryo-EM structure at 3.2 Å of the P. falciparum 80S ribosome with mefloquine; site-directed mutagenesis of binding-site residues\",\n      \"journal\": \"Nature microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM plus functional mutagenesis (Tier 1), but experiments were directed at the mefloquine binding site, not RPL31 specifically; structural membership inferred; single study\",\n      \"pmids\": [\"28288098\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RPL31 (PF3D7_0503800) was visualized as a component of the native P. falciparum 80S ribosome in actively translating states inside infected human erythrocytes, as determined by in situ cryo-electron tomography at high resolution. Eight structures of the ribosome in elongation states were obtained, revealing molecular details of the malarial translation elongation cycle; no specific functional experiment on RPL31 itself was reported beyond its structural membership.\",\n      \"method\": \"In situ cryo-electron tomography of P. falciparum-infected human erythrocytes; eight high-resolution ribosome structures in actively translating states\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in situ cryo-ET at high resolution in native cellular context (Tier 1), but no experiment specifically targeting RPL31; single study\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0503800 (RPL31) is established solely as a structural component of the 60S large subunit of the P. falciparum cytoplasmic 80S ribosome, as visualized by multiple high-resolution cryo-EM and in situ cryo-ET studies; no specific enzymatic activity, binding partner, post-translational modification, or functional role distinct from its ribosome membership has been experimentally defined for this protein.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0503800 (RPL31) is established as a structural component of the 60S large subunit of the Plasmodium falciparum cytoplasmic 80S ribosome, resolved within the assembled ribosome by high-resolution cryo-EM and, in native infected erythrocytes, by in situ cryo-electron tomography of actively translating ribosomes [#0, #3]. Its placement in the large subunit has been reproduced across multiple structural studies of blood-stage ribosomes captured in distinct translational and elongation states [#1, #3], and within structures used to define the ribosomal binding sites of the antimalarials emetine and mefloquine [#0, #2]. Beyond this membership in the 60S subunit, no enzymatic activity, specific binding partner, post-translational modification, or functional role distinct from its structural role in the ribosome has been characterized for PF3D7_0503800 in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Establishing the molecular composition of the P. falciparum ribosome required resolving individual proteins in the assembled complex; RPL31 was placed within the 60S large subunit of the cytoplasmic 80S ribosome.\",\n      \"evidence\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution\",\n      \"pmids\": [\"24913268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional experiment directed at RPL31 itself\", \"Structural membership inferred from ribosome assembly, not from RPL31-specific perturbation\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Whether RPL31's large-subunit placement holds across ribosomes in different translational states was addressed by reconstructing ribosomes purified from blood-stage schizonts in multiple states.\",\n      \"evidence\": \"Cryo-EM reconstruction (sub-nanometer) of schizont ribosomes with flexible fitting of atomic models into five density maps\",\n      \"pmids\": [\"26432834\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional role assigned to RPL31\", \"No perturbation of RPL31 to test its contribution to translation\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Structures used to define antimalarial binding sites reconfirmed RPL31 as a large-subunit component, though the functional mutagenesis targeted the mefloquine site rather than RPL31.\",\n      \"evidence\": \"Cryo-EM structure at 3.2 Å of the 80S ribosome with mefloquine plus site-directed mutagenesis of binding-site residues\",\n      \"pmids\": [\"28288098\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mutagenesis addressed the mefloquine site, not RPL31\", \"No evidence RPL31 contacts or contributes to drug binding\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether RPL31 is a component of native, actively translating ribosomes in the cellular context was addressed by visualizing ribosomes in situ inside infected human erythrocytes.\",\n      \"evidence\": \"In situ cryo-electron tomography of P. falciparum-infected erythrocytes yielding eight ribosome structures in elongation states\",\n      \"pmids\": [\"40825879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No experiment specifically targeting RPL31\", \"Functional contribution of RPL31 to the elongation cycle not tested\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether PF3D7_0503800 has any function, binding partner, or property distinct from its structural membership in the 60S subunit.\",\n      \"evidence\": \"No RPL31-directed functional, genetic, or biochemical experiment exists in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No genetic knockout or knockdown of RPL31\", \"No RPL31-specific binding partners or post-translational modifications identified\", \"No role distinct from ribosome membership defined\"],\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\": [0, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006412\", \"supporting_discovery_ids\": [0, 1, 3]}\n    ],\n    \"complexes\": [\n      \"60S large ribosomal subunit of the P. falciparum cytoplasmic 80S ribosome\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"RPL31 (PF3D7_0503800) is characterized in the available corpus only as a structural component of the 60S large subunit; no binding partner, enzymatic activity, or function distinct from ribosome membership has been experimentally defined.\",\n      \"Structural studies resolving RPL31 also defined the ribosomal binding sites of the antimalarials emetine (E-site, small subunit) [#0] and mefloquine [#2], but no evidence links RPL31 itself to drug binding.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0503800","name":null,"product":"60S ribosomal protein L31","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1103400","name":null,"product":"60S ribosomal protein L31, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1029800","name":null,"product":"60S ribosomal protein L31, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RPL31","evaluation":null}