{"gene":"PF3D7_1424400","run_date":"2026-09-08T14:19:07","timeline":{"discoveries":[{"year":2014,"finding":"PF3D7_1424400 (L7, 60S ribosomal protein L7-3) was resolved as a structural component of the P. falciparum 80S ribosome large subunit at 3.2 Å resolution by cryo-EM; the structure established its membership in the assembled 80S ribosomal complex but did not assign a specific mechanistic role to L7 beyond ribosome composition.","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 establishes ribosome membership, but the abstract does not describe any specific functional experiment directed at L7 itself; membership in the complex is inferred from the structural map","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"finding":"Ribosome heterogeneity studies in Plasmodium parasites indicate that large-subunit proteins including members of the L7 family occupy distinct positions in stage-specific ribosome variants, establishing that 60S ribosomal protein composition (which encompasses L7/PF3D7_1424400) differs across parasite life-cycle stages.","method":"Structural and comparative analysis of stage-specific ribosomes (cryo-EM and proteomics)","journal":"PLoS pathogens","confidence":"Low","confidence_rationale":"Tier 3 / Weak — abstract does not specify L7/PF3D7_1424400 individually; membership in a heterogeneous ribosome pool is inferred from general ribosome-heterogeneity findings","pmids":["37053161"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"In situ cryo-electron tomography of native P. falciparum 80S ribosomes in actively translating states inside infected erythrocytes resolved eight high-resolution structures of the malarial ribosome, within which 60S large-subunit components (including L7/PF3D7_1424400 as a structural constituent) were visualised; perturbation with a Plasmodium-specific translation inhibitor decreased elongation factor-bound ribosomal states and appeared to upregulate ribosome biogenesis.","method":"In situ cryo-electron tomography of native ribosomes in P. falciparum-infected human erythrocytes","journal":"Nature structural & molecular biology","confidence":"Low","confidence_rationale":"Tier 1 / Weak — rigorous structural method but the abstract does not name L7/PF3D7_1424400 specifically; L7 membership in the 80S large subunit is inferred from the general ribosome structural analysis","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1424400 (L7, 60S ribosomal protein L7-3) is established as a structural component of the P. falciparum 80S ribosome large subunit, as visualised by cryo-EM and in situ cryo-electron tomography; no experiment in the available literature has assigned a specific catalytic, regulatory, or binding function to L7 beyond its membership in the assembled ribosomal complex."},"narrative":{"mechanistic_narrative":"PF3D7_1424400 (L7, 60S ribosomal protein L7-3, putative) is a structural component of the large (60S) subunit of the P. falciparum 80S ribosome, established by a 3.2 Å cryo-EM structure that resolved it as a constituent of the assembled ribosomal complex without assigning it a distinct catalytic or regulatory role beyond ribosome composition [PMID:24913268]. Beyond this membership assignment, no experiment in the available corpus assigns a specific binding partner, substrate, or independent function to L7 itself; broader analyses of stage-specific ribosome heterogeneity and in situ translating-ribosome states place 60S large-subunit proteins of the L7 family in the malarial ribosome but do not characterize PF3D7_1424400 individually [PMID:37053161, PMID:40825879]. No further mechanistic detail specific to L7 has been characterized in the available corpus.","teleology":[{"year":2014,"claim":"Whether L7/PF3D7_1424400 is part of the assembled P. falciparum ribosome was resolved by placing it structurally within the 60S large subunit, establishing it as a bona fide ribosomal protein of the parasite 80S complex.","evidence":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution","pmids":["24913268"],"confidence":"Medium","gaps":["No specific catalytic, regulatory, or binding function assigned to L7 beyond ribosome membership","No experiment directed at L7 itself; role inferred from the structural map","No interaction partners or substrates identified for L7 individually"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"claim":"Whether 60S ribosomal protein composition varies across the parasite life cycle was addressed by ribosome-heterogeneity analysis, placing L7-family large-subunit proteins in distinct stage-specific ribosome variants, though not resolving L7/PF3D7_1424400 individually.","evidence":"Structural and comparative analysis of stage-specific Plasmodium ribosomes (cryo-EM and proteomics)","pmids":["37053161"],"confidence":"Low","gaps":["Abstract does not specify L7/PF3D7_1424400 individually; membership in the heterogeneous pool is inferred from general L7-family findings","No functional consequence attributed to L7 in any specific life-cycle stage","Whether L7 itself is present or absent in specific variants is not established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Whether native, actively translating parasite ribosomes could be visualised in their cellular context was addressed by in situ cryo-electron tomography, resolving 60S large-subunit components including L7 as structural constituents of translating 80S ribosomes.","evidence":"In situ cryo-electron tomography of native ribosomes in P. falciparum-infected human erythrocytes, with perturbation by a Plasmodium-specific translation inhibitor","pmids":["40825879"],"confidence":"Low","gaps":["Abstract does not name L7/PF3D7_1424400 specifically; membership inferred from general 80S large-subunit analysis","No L7-specific contribution to elongation-factor binding or ribosome biogenesis established","The inhibitor effect is a ribosome-level observation, not an L7-directed one"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether L7/PF3D7_1424400 has any function beyond being a structural component of the 60S subunit — a specific role in assembly, translation regulation, or non-ribosomal activity — remains unaddressed.","evidence":"","pmids":[],"confidence":"Low","gaps":["No experiment isolates or perturbs L7 individually","No binding partners or substrates identified for L7 beyond the ribosome","No genetic or biochemical test of L7 essentiality or function"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["P. falciparum 80S ribosome large (60S) subunit"],"partners":[],"other_free_text":["Established only as a structural constituent of the assembled P. falciparum 80S ribosome large subunit; no independent function, partner, or substrate assigned to PF3D7_1424400 in the available corpus.","L7-family 60S proteins occupy positions in stage-specific ribosome variants, but PF3D7_1424400 is not individually characterized in the heterogeneity or in situ tomography studies."]}},"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":"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":136,"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":"20078859","id":"PMC_20078859","title":"Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum.","date":"2010","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/20078859","citation_count":12,"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 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repeats.","date":"2020","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/32469313","citation_count":21,"is_preprint":false,"source_species":["Pf"],"role":"citation_expansion","match_terms":["fwd_cite"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"37053161","id":"PMC_37053161","title":"Ribosome heterogeneity and specialization of Plasmodium parasites.","date":"2023","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/37053161","citation_count":13,"is_preprint":false,"source_species":["Pf"],"role":"citation_expansion","match_terms":["fwd_cite"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"31866984","id":"PMC_31866984","title":"Adaptation of Translational Machinery in Malaria Parasites to Accommodate Translation of Poly-Adenosine Stretches Throughout Its Life Cycle.","date":"2019","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/31866984","citation_count":11,"is_preprint":false,"source_species":["Pf"],"role":"citation_expansion","match_terms":["fwd_cite"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34017052","id":"PMC_34017052","title":"Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation.","date":"2021","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/34017052","citation_count":6,"is_preprint":false,"source_species":["Pf"],"role":"citation_expansion","match_terms":["fwd_cite"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41315737","id":"PMC_41315737","title":"MAP-X reveals distinct protein complex dynamics across Plasmodium falciparum blood stages.","date":"2025","source":"Nature microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/41315737","citation_count":2,"is_preprint":false,"source_species":["Pf"],"role":"citation_expansion","match_terms":["fwd_cite"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"42001110","id":"PMC_42001110","title":"Targeting protein-protein interactions in Plasmodium: from asexual replication to sexual development.","date":"2026","source":"Parasites & vectors","url":"https://pubmed.ncbi.nlm.nih.gov/42001110","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"citation_expansion","match_terms":["fwd_cite"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7712,"output_tokens":987,"usd":0.018971,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5711,"output_tokens":1910,"usd":0.038152,"stage2_stop_reason":"end_turn"},"total_usd":0.057123,"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\": \"PF3D7_1424400 (L7, 60S ribosomal protein L7-3) was resolved as a structural component of the P. falciparum 80S ribosome large subunit at 3.2 Å resolution by cryo-EM; the structure established its membership in the assembled 80S ribosomal complex but did not assign a specific mechanistic role to L7 beyond ribosome composition.\",\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 establishes ribosome membership, but the abstract does not describe any specific functional experiment directed at L7 itself; membership in the complex is inferred from the structural map\",\n      \"pmids\": [\"24913268\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Ribosome heterogeneity studies in Plasmodium parasites indicate that large-subunit proteins including members of the L7 family occupy distinct positions in stage-specific ribosome variants, establishing that 60S ribosomal protein composition (which encompasses L7/PF3D7_1424400) differs across parasite life-cycle stages.\",\n      \"method\": \"Structural and comparative analysis of stage-specific ribosomes (cryo-EM and proteomics)\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — abstract does not specify L7/PF3D7_1424400 individually; membership in a heterogeneous ribosome pool is inferred from general ribosome-heterogeneity findings\",\n      \"pmids\": [\"37053161\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In situ cryo-electron tomography of native P. falciparum 80S ribosomes in actively translating states inside infected erythrocytes resolved eight high-resolution structures of the malarial ribosome, within which 60S large-subunit components (including L7/PF3D7_1424400 as a structural constituent) were visualised; perturbation with a Plasmodium-specific translation inhibitor decreased elongation factor-bound ribosomal states and appeared to upregulate ribosome biogenesis.\",\n      \"method\": \"In situ cryo-electron tomography of native ribosomes in P. falciparum-infected human erythrocytes\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 1 / Weak — rigorous structural method but the abstract does not name L7/PF3D7_1424400 specifically; L7 membership in the 80S large subunit is inferred from the general ribosome structural analysis\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1424400 (L7, 60S ribosomal protein L7-3) is established as a structural component of the P. falciparum 80S ribosome large subunit, as visualised by cryo-EM and in situ cryo-electron tomography; no experiment in the available literature has assigned a specific catalytic, regulatory, or binding function to L7 beyond its membership in the assembled ribosomal complex.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1424400 (L7, 60S ribosomal protein L7-3, putative) is a structural component of the large (60S) subunit of the P. falciparum 80S ribosome, established by a 3.2 Å cryo-EM structure that resolved it as a constituent of the assembled ribosomal complex without assigning it a distinct catalytic or regulatory role beyond ribosome composition [#0]. Beyond this membership assignment, no experiment in the available corpus assigns a specific binding partner, substrate, or independent function to L7 itself; broader analyses of stage-specific ribosome heterogeneity and in situ translating-ribosome states place 60S large-subunit proteins of the L7 family in the malarial ribosome but do not characterize PF3D7_1424400 individually [#1, #2]. No further mechanistic detail specific to L7 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Whether L7/PF3D7_1424400 is part of the assembled P. falciparum ribosome was resolved by placing it structurally within the 60S large subunit, establishing it as a bona fide ribosomal protein of the parasite 80S complex.\",\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 specific catalytic, regulatory, or binding function assigned to L7 beyond ribosome membership\",\n        \"No experiment directed at L7 itself; role inferred from the structural map\",\n        \"No interaction partners or substrates identified for L7 individually\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Whether 60S ribosomal protein composition varies across the parasite life cycle was addressed by ribosome-heterogeneity analysis, placing L7-family large-subunit proteins in distinct stage-specific ribosome variants, though not resolving L7/PF3D7_1424400 individually.\",\n      \"evidence\": \"Structural and comparative analysis of stage-specific Plasmodium ribosomes (cryo-EM and proteomics)\",\n      \"pmids\": [\"37053161\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Abstract does not specify L7/PF3D7_1424400 individually; membership in the heterogeneous pool is inferred from general L7-family findings\",\n        \"No functional consequence attributed to L7 in any specific life-cycle stage\",\n        \"Whether L7 itself is present or absent in specific variants is not established\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether native, actively translating parasite ribosomes could be visualised in their cellular context was addressed by in situ cryo-electron tomography, resolving 60S large-subunit components including L7 as structural constituents of translating 80S ribosomes.\",\n      \"evidence\": \"In situ cryo-electron tomography of native ribosomes in P. falciparum-infected human erythrocytes, with perturbation by a Plasmodium-specific translation inhibitor\",\n      \"pmids\": [\"40825879\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Abstract does not name L7/PF3D7_1424400 specifically; membership inferred from general 80S large-subunit analysis\",\n        \"No L7-specific contribution to elongation-factor binding or ribosome biogenesis established\",\n        \"The inhibitor effect is a ribosome-level observation, not an L7-directed one\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether L7/PF3D7_1424400 has any function beyond being a structural component of the 60S subunit — a specific role in assembly, translation regulation, or non-ribosomal activity — remains unaddressed.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No experiment isolates or perturbs L7 individually\",\n        \"No binding partners or substrates identified for L7 beyond the ribosome\",\n        \"No genetic or biochemical test of L7 essentiality or function\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003735\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0022625\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006412\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\n      \"P. falciparum 80S ribosome large (60S) subunit\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Established only as a structural constituent of the assembled P. falciparum 80S ribosome large subunit; no independent function, partner, or substrate assigned to PF3D7_1424400 in the available corpus.\",\n      \"L7-family 60S proteins occupy positions in stage-specific ribosome variants, but PF3D7_1424400 is not individually characterized in the heterogeneity or in situ tomography studies.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1424400","name":null,"product":"60S ribosomal protein L7-3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1019400","name":null,"product":"60S ribosomal protein L7-3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1333700","name":null,"product":"ribosomal protein L7A, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}