{"gene":"PF3D7_1144300","run_date":"2026-09-08T14:19:05","timeline":{"discoveries":[{"year":2014,"finding":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution was determined, within which RPL41 (PF3D7_1144300) is present as a component of the large (60S) subunit. The structure establishes RPL41's membership in the assembled cytoplasmic ribosome of P. falciparum, but no specific functional role for RPL41 beyond its structural presence in the complex is described.","method":"Cryo-EM structure determination at 3.2 Å resolution","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM structure establishes structural membership, but no functional characterization specific to RPL41 is reported; single study","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"Five cryo-EM reconstructions of the P. falciparum 80S ribosome from blood-stage schizonts at sub-nanometer resolution were obtained, with atomic models built by flexible fitting. RPL41 (PF3D7_1144300) is a structural component of the 60S large subunit within these ribosomal complexes, but no specific functional detail about RPL41 itself is reported beyond its structural presence.","method":"Cryo-EM reconstruction and flexible-fitting atomic modeling","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — structural methodology is rigorous but no RPL41-specific functional data are provided; single study","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 in complex with (+)-mefloquine was determined; RPL41 (PF3D7_1144300) is a component of the 60S subunit within this structure. No specific functional role for RPL41 beyond structural membership in the complex is described.","method":"Cryo-EM structure determination at 3.2 Å, mutagenesis of binding-site residues","journal":"Nature microbiology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM establishes structural context, but no functional characterization specific to RPL41 is reported; single study","pmids":["28288098"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"Eight high-resolution in situ cryo-electron tomography structures of the native P. falciparum 80S ribosome in actively translating states inside infected erythrocytes were determined. RPL41 (PF3D7_1144300) is a structural constituent of the 60S large subunit observed in these native translating ribosome complexes. No RPL41-specific functional data beyond structural membership are reported.","method":"In situ cryo-electron tomography of native translating ribosomes inside P. falciparum-infected erythrocytes","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — state-of-the-art in situ structural approach, but no mechanistic detail specific to RPL41 is reported; single study","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"RPL41 (PF3D7_1144300) is established as a structural component of the 60S large subunit of the P. falciparum cytoplasmic 80S ribosome, as shown by multiple high-resolution cryo-EM and in situ cryo-ET structures; no specific enzymatic activity, binding partners, post-translational modifications, or individual functional role for RPL41 beyond its membership in the assembled ribosomal complex have been mechanistically characterized."},"narrative":{"mechanistic_narrative":"RPL41 (PF3D7_1144300) is a structural component of the 60S large subunit of the Plasmodium falciparum cytoplasmic 80S ribosome, established through successive high-resolution cryo-EM and in situ cryo-electron tomography structures of the assembled ribosome [PMID:24913268, PMID:40825879]. It is observed within the 60S subunit in structures of the free ribosome [PMID:24913268, PMID:26432834], in complex with the antimalarial (+)-mefloquine [PMID:28288098], and in native, actively translating ribosomes imaged inside infected erythrocytes [PMID:40825879]. Beyond this membership in the assembled ribosomal complex, no specific enzymatic activity, binding partners, post-translational modifications, or individual functional role for RPL41 has been characterized in the available corpus.","teleology":[{"year":2014,"claim":"Whether RPL41 is a constituent of the P. falciparum cytoplasmic ribosome was resolved by placing it structurally within the assembled 80S particle.","evidence":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å, within which RPL41 is a 60S subunit component","pmids":["24913268"],"confidence":"Medium","gaps":["No RPL41-specific function is assigned beyond structural presence","No individual binding partners or contacts of RPL41 are described","No perturbation or knockout of RPL41 to test its functional role"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"Structural placement of RPL41 in the 60S subunit was reinforced across multiple ribosome states from blood-stage schizonts, confirming it is a stable constituent rather than a transient factor.","evidence":"Five sub-nanometer cryo-EM reconstructions with flexible-fitting atomic models of schizont-derived 80S ribosomes","pmids":["26432834"],"confidence":"Medium","gaps":["No functional detail specific to RPL41 reported","Role of RPL41 in any translational state not distinguished"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2017,"claim":"RPL41 remains a resolved 60S component in the drug-bound ribosome, situating it within the pharmacologically targeted particle even though it is not itself implicated as the drug-binding site.","evidence":"Cryo-EM structure of the 80S ribosome at 3.2 Å bound to (+)-mefloquine, with binding-site residue mutagenesis","pmids":["28288098"],"confidence":"Medium","gaps":["RPL41 is not shown to contribute to the mefloquine binding site","No functional consequence of drug binding attributed to RPL41"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Whether RPL41 is present in native, actively translating ribosomes in their cellular context was answered by resolving it in situ inside infected erythrocytes.","evidence":"Eight high-resolution in situ cryo-electron tomography structures of native translating 80S ribosomes inside P. falciparum-infected erythrocytes","pmids":["40825879"],"confidence":"Medium","gaps":["No RPL41-specific mechanistic role in translation elongation established","No interactions unique to RPL41 resolved within translating states"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"It remains unknown whether RPL41 has any function, binding partner, or phenotype beyond its structural membership in the 60S subunit.","evidence":"No functional, genetic, or biochemical characterization of RPL41 exists in the available corpus","pmids":[],"confidence":"Medium","gaps":["No genetic knockout or knockdown of RPL41","No RPL41-specific binding partners or post-translational modifications identified","No role in ribosome assembly, translational fidelity, or drug response demonstrated"],"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":["RPL41 is resolved within the 80S ribosome in complex with the antimalarial (+)-mefloquine, but is not shown to contribute to the drug-binding site [#2].","No function for RPL41 beyond its structural membership in the assembled 60S subunit has been characterized in the available corpus."]}},"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":9672,"output_tokens":1684,"usd":0.043257,"retried_sync":true},"stage2":{"model":"claude-opus-4-8","input_tokens":5985,"output_tokens":1957,"usd":0.039425,"stage2_stop_reason":"end_turn"},"total_usd":0.082682,"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 determined, within which RPL41 (PF3D7_1144300) is present as a component of the large (60S) subunit. The structure establishes RPL41's membership in the assembled cytoplasmic ribosome of P. falciparum, but no specific functional role for RPL41 beyond its structural presence in the complex is described.\",\n      \"method\": \"Cryo-EM structure determination at 3.2 Å resolution\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM structure establishes structural membership, but no functional characterization specific to RPL41 is reported; single study\",\n      \"pmids\": [\"24913268\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Five cryo-EM reconstructions of the P. falciparum 80S ribosome from blood-stage schizonts at sub-nanometer resolution were obtained, with atomic models built by flexible fitting. RPL41 (PF3D7_1144300) is a structural component of the 60S large subunit within these ribosomal complexes, but no specific functional detail about RPL41 itself is reported beyond its structural presence.\",\n      \"method\": \"Cryo-EM reconstruction and flexible-fitting atomic modeling\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — structural methodology is rigorous but no RPL41-specific functional data are provided; single study\",\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 in complex with (+)-mefloquine was determined; RPL41 (PF3D7_1144300) is a component of the 60S subunit within this structure. No specific functional role for RPL41 beyond structural membership in the complex is described.\",\n      \"method\": \"Cryo-EM structure determination at 3.2 Å, mutagenesis of binding-site residues\",\n      \"journal\": \"Nature microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM establishes structural context, but no functional characterization specific to RPL41 is reported; single study\",\n      \"pmids\": [\"28288098\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Eight high-resolution in situ cryo-electron tomography structures of the native P. falciparum 80S ribosome in actively translating states inside infected erythrocytes were determined. RPL41 (PF3D7_1144300) is a structural constituent of the 60S large subunit observed in these native translating ribosome complexes. No RPL41-specific functional data beyond structural membership are reported.\",\n      \"method\": \"In situ cryo-electron tomography of native translating ribosomes inside P. falciparum-infected erythrocytes\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — state-of-the-art in situ structural approach, but no mechanistic detail specific to RPL41 is reported; single study\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"RPL41 (PF3D7_1144300) is established as a structural component of the 60S large subunit of the P. falciparum cytoplasmic 80S ribosome, as shown by multiple high-resolution cryo-EM and in situ cryo-ET structures; no specific enzymatic activity, binding partners, post-translational modifications, or individual functional role for RPL41 beyond its membership in the assembled ribosomal complex have been mechanistically characterized.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPL41 (PF3D7_1144300) is a structural component of the 60S large subunit of the Plasmodium falciparum cytoplasmic 80S ribosome, established through successive high-resolution cryo-EM and in situ cryo-electron tomography structures of the assembled ribosome [#0, #3]. It is observed within the 60S subunit in structures of the free ribosome [#0, #1], in complex with the antimalarial (+)-mefloquine [#2], and in native, actively translating ribosomes imaged inside infected erythrocytes [#3]. Beyond this membership in the assembled ribosomal complex, no specific enzymatic activity, binding partners, post-translational modifications, or individual functional role for RPL41 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Whether RPL41 is a constituent of the P. falciparum cytoplasmic ribosome was resolved by placing it structurally within the assembled 80S particle.\",\n      \"evidence\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å, within which RPL41 is a 60S subunit component\",\n      \"pmids\": [\"24913268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No RPL41-specific function is assigned beyond structural presence\",\n        \"No individual binding partners or contacts of RPL41 are described\",\n        \"No perturbation or knockout of RPL41 to test its functional role\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Structural placement of RPL41 in the 60S subunit was reinforced across multiple ribosome states from blood-stage schizonts, confirming it is a stable constituent rather than a transient factor.\",\n      \"evidence\": \"Five sub-nanometer cryo-EM reconstructions with flexible-fitting atomic models of schizont-derived 80S ribosomes\",\n      \"pmids\": [\"26432834\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional detail specific to RPL41 reported\",\n        \"Role of RPL41 in any translational state not distinguished\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"RPL41 remains a resolved 60S component in the drug-bound ribosome, situating it within the pharmacologically targeted particle even though it is not itself implicated as the drug-binding site.\",\n      \"evidence\": \"Cryo-EM structure of the 80S ribosome at 3.2 Å bound to (+)-mefloquine, with binding-site residue mutagenesis\",\n      \"pmids\": [\"28288098\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"RPL41 is not shown to contribute to the mefloquine binding site\",\n        \"No functional consequence of drug binding attributed to RPL41\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether RPL41 is present in native, actively translating ribosomes in their cellular context was answered by resolving it in situ inside infected erythrocytes.\",\n      \"evidence\": \"Eight high-resolution in situ cryo-electron tomography structures of native translating 80S ribosomes inside P. falciparum-infected erythrocytes\",\n      \"pmids\": [\"40825879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No RPL41-specific mechanistic role in translation elongation established\",\n        \"No interactions unique to RPL41 resolved within translating states\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether RPL41 has any function, binding partner, or phenotype beyond its structural membership in the 60S subunit.\",\n      \"evidence\": \"No functional, genetic, or biochemical characterization of RPL41 exists in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No genetic knockout or knockdown of RPL41\",\n        \"No RPL41-specific binding partners or post-translational modifications identified\",\n        \"No role in ribosome assembly, translational fidelity, or drug response demonstrated\"\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      \"RPL41 is resolved within the 80S ribosome in complex with the antimalarial (+)-mefloquine, but is not shown to contribute to the drug-binding site [#2].\",\n      \"No function for RPL41 beyond its structural membership in the assembled 60S subunit has been characterized in the available corpus.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1144300","name":null,"product":"60S ribosomal protein L41","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0904700","name":null,"product":"60S ribosomal protein L41, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RPL41","evaluation":null}