{"gene":"PF3D7_0516900","run_date":"2026-09-07T10:55:52","timeline":{"discoveries":[{"year":2014,"finding":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution revealed that L2 (PF3D7_0516900) is a component of the large 60S ribosomal subunit within the intact malarial cytoplasmic ribosome complex bound to emetine.","method":"Cryo-EM structure determination at 3.2 Å resolution","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM structure of the intact ribosome establishes subunit composition including L2, but the abstract does not report specific functional experiments on L2 itself; single study","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"finding":"Ribosome heterogeneity studies in Plasmodium parasites place L2 (PF3D7_0516900) as a constituent of the 60S large subunit of heterogeneous ribosome populations across parasite life-cycle stages.","method":"Structural and compositional analysis of stage-specific ribosomes","journal":"PLoS pathogens","confidence":"Low","confidence_rationale":"Tier 3 / Weak — abstract-level mention of ribosome composition without specific functional characterization of L2 itself; single study","pmids":["37053161"],"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, establishing that L2 (PF3D7_0516900) is a structural component of the large 60S subunit within the physiologically translating ribosome in its native cellular context.","method":"In situ cryo-electron tomography inside P. falciparum-infected human erythrocytes","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution in situ structural study establishes ribosome composition including the 60S subunit, but no specific functional experiment targets L2 individually; single study","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0516900 (L2) is a structural component of the P. falciparum 60S large ribosomal subunit within the cytoplasmic 80S ribosome, as established by cryo-EM and in situ cryo-electron tomography studies of the malarial translation machinery; no specific catalytic or regulatory function has been experimentally assigned to L2 itself beyond its membership in the 60S subunit."},"narrative":{"mechanistic_narrative":"PF3D7_0516900 (L2) is a structural constituent of the large 60S subunit of the Plasmodium falciparum cytoplasmic 80S ribosome, resolved as a component of the intact malarial ribosome by cryo-EM [PMID:24913268] and confirmed as part of the natively translating ribosome by in situ cryo-electron tomography inside infected erythrocytes [PMID:40825879]. It is also present in heterogeneous ribosome populations across parasite life-cycle stages [PMID:37053161]. Beyond its assignment as a 60S subunit component, no specific catalytic or regulatory function has been experimentally characterized for L2 itself in the available corpus.","teleology":[{"year":2014,"claim":"Establishing the subunit composition of the malarial ribosome placed L2 within the 60S large subunit of the intact cytoplasmic 80S ribosome, defining its basic structural membership.","evidence":"Cryo-EM structure determination of the emetine-bound P. falciparum 80S ribosome at 3.2 Å resolution","pmids":["24913268"],"confidence":"Medium","gaps":["No functional experiment targets L2 individually","No catalytic or regulatory role assigned","Does not address stage-specific variation"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2023,"claim":"Assessing ribosome heterogeneity across the life cycle tested whether L2 is a constant or variable component, placing it among constituents of heterogeneous 60S subunits in stage-specific ribosome populations.","evidence":"Structural and compositional analysis of stage-specific Plasmodium ribosomes","pmids":["37053161"],"confidence":"Low","gaps":["Abstract-level compositional mention without functional characterization of L2","Does not establish whether L2 occupancy itself varies","No mechanism linking heterogeneity to translation"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Resolving the ribosome in its native cellular context confirmed that L2 is a structural component of the 60S subunit within physiologically translating ribosomes, extending the in vitro assignment to actively translating states in situ.","evidence":"In situ cryo-electron tomography of ribosomes inside P. falciparum-infected human erythrocytes, yielding eight high-resolution translating-state structures","pmids":["40825879"],"confidence":"Medium","gaps":["No functional experiment isolates L2's contribution to translation","No structural role for L2 within the subunit is dissected","Does not address essentiality or drug targeting of L2"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether L2 has any function beyond serving as a 60S structural component — including essentiality, assembly role, or contribution to ribosome heterogeneity — remains uncharacterized.","evidence":"No direct functional study of L2 exists in the corpus","pmids":[],"confidence":"Low","gaps":["No gene knockdown/knockout of L2","No assembly or biogenesis role established","No specific catalytic or regulatory activity assigned"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["60S large ribosomal subunit","cytoplasmic 80S ribosome"],"partners":[],"other_free_text":["L2 is present in heterogeneous ribosome populations across P. falciparum life-cycle stages [#1].","No function beyond membership in the 60S subunit has been experimentally assigned to L2 itself 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 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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":14,"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":12,"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":8,"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":"28540920","id":"PMC_28540920","title":"Parasite physiology: No longer lost in translation.","date":"2017","source":"Nature microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/28540920","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":6313,"output_tokens":845,"usd":0.015807,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5509,"output_tokens":1619,"usd":0.03401,"stage2_stop_reason":"end_turn"},"total_usd":0.049817,"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\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution revealed that L2 (PF3D7_0516900) is a component of the large 60S ribosomal subunit within the intact malarial cytoplasmic ribosome complex bound to emetine.\",\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 of the intact ribosome establishes subunit composition including L2, but the abstract does not report specific functional experiments on L2 itself; single study\",\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 place L2 (PF3D7_0516900) as a constituent of the 60S large subunit of heterogeneous ribosome populations across parasite life-cycle stages.\",\n      \"method\": \"Structural and compositional analysis of stage-specific ribosomes\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — abstract-level mention of ribosome composition without specific functional characterization of L2 itself; single study\",\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 P. falciparum-infected erythrocytes resolved eight high-resolution structures of the native malarial ribosome in actively translating states, establishing that L2 (PF3D7_0516900) is a structural component of the large 60S subunit within the physiologically translating ribosome in its native cellular context.\",\n      \"method\": \"In situ cryo-electron tomography inside P. falciparum-infected human erythrocytes\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution in situ structural study establishes ribosome composition including the 60S subunit, but no specific functional experiment targets L2 individually; single study\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_0516900 (L2) is a structural component of the P. falciparum 60S large ribosomal subunit within the cytoplasmic 80S ribosome, as established by cryo-EM and in situ cryo-electron tomography studies of the malarial translation machinery; no specific catalytic or regulatory function has been experimentally assigned to L2 itself beyond its membership in the 60S subunit.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0516900 (L2) is a structural constituent of the large 60S subunit of the Plasmodium falciparum cytoplasmic 80S ribosome, resolved as a component of the intact malarial ribosome by cryo-EM [#0] and confirmed as part of the natively translating ribosome by in situ cryo-electron tomography inside infected erythrocytes [#2]. It is also present in heterogeneous ribosome populations across parasite life-cycle stages [#1]. Beyond its assignment as a 60S subunit component, no specific catalytic or regulatory function has been experimentally characterized for L2 itself in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Establishing the subunit composition of the malarial ribosome placed L2 within the 60S large subunit of the intact cytoplasmic 80S ribosome, defining its basic structural membership.\",\n      \"evidence\": \"Cryo-EM structure determination of the emetine-bound P. falciparum 80S ribosome at 3.2 Å resolution\",\n      \"pmids\": [\"24913268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional experiment targets L2 individually\",\n        \"No catalytic or regulatory role assigned\",\n        \"Does not address stage-specific variation\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Assessing ribosome heterogeneity across the life cycle tested whether L2 is a constant or variable component, placing it among constituents of heterogeneous 60S subunits in stage-specific ribosome populations.\",\n      \"evidence\": \"Structural and compositional analysis of stage-specific Plasmodium ribosomes\",\n      \"pmids\": [\"37053161\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Abstract-level compositional mention without functional characterization of L2\",\n        \"Does not establish whether L2 occupancy itself varies\",\n        \"No mechanism linking heterogeneity to translation\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Resolving the ribosome in its native cellular context confirmed that L2 is a structural component of the 60S subunit within physiologically translating ribosomes, extending the in vitro assignment to actively translating states in situ.\",\n      \"evidence\": \"In situ cryo-electron tomography of ribosomes inside P. falciparum-infected human erythrocytes, yielding eight high-resolution translating-state structures\",\n      \"pmids\": [\"40825879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional experiment isolates L2's contribution to translation\",\n        \"No structural role for L2 within the subunit is dissected\",\n        \"Does not address essentiality or drug targeting of L2\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether L2 has any function beyond serving as a 60S structural component — including essentiality, assembly role, or contribution to ribosome heterogeneity — remains uncharacterized.\",\n      \"evidence\": \"No direct functional study of L2 exists in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No gene knockdown/knockout of L2\",\n        \"No assembly or biogenesis role established\",\n        \"No specific catalytic or regulatory activity assigned\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003735\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0022625\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0005737\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006412\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\n      \"60S large ribosomal subunit\",\n      \"cytoplasmic 80S ribosome\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"L2 is present in heterogeneous ribosome populations across P. falciparum life-cycle stages [#1].\",\n      \"No function beyond membership in the 60S subunit has been experimentally assigned to L2 itself in the available corpus.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0516900","name":null,"product":"60S ribosomal protein L2","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1231700","name":null,"product":"60S ribosomal protein L2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1016400","name":null,"product":"60S ribosomal protein L2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}