{"gene":"PF3D7_0821700","run_date":"2026-09-08T12:51:27","timeline":{"discoveries":[{"year":2006,"finding":"PF3D7_0821700 (PfRpl22/L22), the nuclear genome-encoded large subunit ribosomal protein L22, is predicted to associate with the apicoplast-encoded ribosomal protein L4 (PfRpl4) and the large subunit rRNA to form the 50S ribosome polypeptide exit tunnel that can be occupied by azithromycin. Resistance selection experiments showed that the PfRpl22 sequence remained unchanged in azithromycin-resistant lines, while mutations in PfRpl4 altered the tunnel, implying L22's structural role in the exit tunnel but not as a direct resistance determinant.","method":"In vitro resistance selection, sequencing of resistant parasite lines, molecular modeling of the polypeptide exit tunnel","journal":"The Journal of biological chemistry","confidence":"Low","confidence_rationale":"Tier 4 / Weak — structural role inferred from molecular modeling and absence of mutations in L22 in resistant lines; no direct biochemical assay of L22 function performed","pmids":["17110371"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"7G8"},{"species":"Plasmodium falciparum","strain":"Dd2"}]},{"year":2014,"finding":"L22 (PF3D7_0821700) was resolved as a component of the P. falciparum 80S ribosome large subunit in the first atomic-resolution cryo-EM structure of the parasite ribosome, placing it structurally within the cytoplasmic 60S ribosomal particle.","method":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-resolution cryo-EM structure establishes complex membership, but single study and L22 is not the focus; no mutagenesis or functional validation specific to L22","pmids":["24913268"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"finding":"L22 (PF3D7_0821700) was incorporated into atomic models built from cryo-EM reconstructions of P. falciparum 80S ribosomes purified from blood-stage schizonts, confirming its structural presence in the large subunit of the translating ribosome.","method":"Cryo-EM reconstructions at sub-nanometer resolution with flexible fitting of atomic models from P. falciparum schizont-purified ribosomes","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — structural placement via cryo-EM atomic model, single study, no functional assay specific to L22","pmids":["26432834"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"L22 (PF3D7_0821700) is present as a structural component of the native P. falciparum 80S ribosome in actively translating states, as visualized in situ inside infected human erythrocytes by high-resolution cryo-electron tomography.","method":"In situ cryo-electron tomography of P. falciparum-infected human erythrocytes; eight high-resolution structures of the native malarial ribosome in actively translating states","journal":"Nature structural & molecular biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in situ high-resolution structural data confirms ribosome membership in the native cellular context, but L22 is not individually studied functionally; single study","pmids":["40825879"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0821700 (L22) is a structural component of the 60S large subunit of the P. falciparum cytoplasmic 80S ribosome, visualized in multiple cryo-EM and cryo-ET structures of the parasite ribosome in both isolated and native in-cell translating states; it is predicted by molecular modeling to contribute to the polypeptide exit tunnel together with PfRpl4, but no direct biochemical or mutagenesis experiments have defined a unique function for L22 beyond its ribosomal structural membership."},"narrative":{"mechanistic_narrative":"PF3D7_0821700 (L22) is a nuclear genome-encoded large-subunit ribosomal protein that serves as a structural component of the 60S large subunit of the P. falciparum cytoplasmic 80S ribosome [PMID:24913268]. It has been resolved within the large subunit in successive high-resolution cryo-EM structures of the parasite ribosome purified from blood-stage schizonts [PMID:24913268, PMID:26432834] and visualized in situ in actively translating native ribosomes inside infected human erythrocytes by cryo-electron tomography [PMID:40825879]. Molecular modeling predicts that L22 contributes together with the apicoplast-encoded PfRpl4 to the polypeptide exit tunnel that can be occupied by azithromycin, and in vitro azithromycin-resistance selection left the L22 sequence unchanged while mutations arose in PfRpl4, indicating a structural exit-tunnel role for L22 rather than a direct drug-resistance determinant [PMID:17110371]. Beyond its membership in the ribosomal large subunit and its predicted exit-tunnel contribution, no direct biochemical or mutagenesis experiments defining a unique function for L22 have been characterized in the available corpus.","teleology":[{"year":2006,"claim":"To locate the target of azithromycin action in the parasite, resistance selection tested whether L22, predicted to line the polypeptide exit tunnel, was itself a resistance determinant, establishing L22's inferred structural role in the tunnel while excluding it as a mutational drug-resistance site.","evidence":"In vitro azithromycin resistance selection with sequencing of resistant lines and molecular modeling of the exit tunnel in P. falciparum 7G8 and Dd2","pmids":["17110371"],"confidence":"Low","gaps":["Structural role inferred from modeling and absence of mutations, not from direct biochemical assay of L22","No mutagenesis of L22 to test its exit-tunnel contribution","Interaction with PfRpl4 predicted, not experimentally demonstrated"],"attribution":[{"species":"Plasmodium falciparum","strain":"7G8"},{"species":"Plasmodium falciparum","strain":"Dd2"}]},{"year":2014,"claim":"The first atomic-resolution cryo-EM structure of the parasite ribosome resolved where L22 sits, placing it definitively within the cytoplasmic 60S large subunit rather than in any other complex.","evidence":"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution","pmids":["24913268"],"confidence":"Medium","gaps":["L22 was not the focus and received no functional validation","No mutagenesis linking its position to a specific translational function"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2015,"claim":"Cryo-EM reconstructions from schizont-purified ribosomes confirmed L22 as a stable structural member of the translating large subunit, reinforcing its ribosomal assignment across biological samples.","evidence":"Cryo-EM reconstructions with flexible fitting of atomic models from P. falciparum schizont-purified ribosomes","pmids":["26432834"],"confidence":"Medium","gaps":["No functional assay specific to L22","Does not distinguish L22's role from that of neighboring large-subunit proteins"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"In situ cryo-electron tomography confirmed that L22 is a component of native, actively translating ribosomes in their cellular context, extending its structural assignment from purified particles to the intact parasite.","evidence":"In situ cryo-electron tomography of P. falciparum-infected human erythrocytes yielding eight high-resolution structures of the native ribosome in translating states","pmids":["40825879"],"confidence":"Medium","gaps":["L22 not individually studied functionally","No perturbation to test its contribution to translation in vivo"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether L22 has any function beyond structural membership in the 60S subunit — including a directly demonstrated contribution to the polypeptide exit tunnel or an interaction with PfRpl4 — remains unresolved.","evidence":"No direct biochemical or mutagenesis experiments on L22 exist in the corpus","pmids":[],"confidence":"Low","gaps":["No mutagenesis or knockdown of L22","No biochemical demonstration of the predicted L22–PfRpl4 exit-tunnel interaction","No extra-ribosomal or moonlighting role tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["60S large ribosomal subunit of the cytoplasmic 80S ribosome"],"partners":["PFRPL4 (PREDICTED EXIT-TUNNEL CO-CONTRIBUTOR, MOLECULAR MODELING ONLY) [#0]"],"other_free_text":["Predicted to contribute to the polypeptide exit tunnel occupied by azithromycin; L22 sequence unchanged in azithromycin-resistant lines, so not a direct resistance determinant [#0]","Structural membership established by cryo-EM (2014, 2015) and in situ cryo-ET (2025); no direct functional or mutagenesis data specific to L22 in the 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":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":"17110371","id":"PMC_17110371","title":"In vitro efficacy, resistance selection, and structural modeling studies implicate the malarial parasite apicoplast as the target of azithromycin.","date":"2006","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/17110371","citation_count":125,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["L22"],"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":"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":7,"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":3,"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":5436,"output_tokens":1273,"usd":0.017701,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6100,"output_tokens":2376,"usd":0.04495,"stage2_stop_reason":"end_turn"},"total_usd":0.062651,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"PF3D7_0821700 (PfRpl22/L22), the nuclear genome-encoded large subunit ribosomal protein L22, is predicted to associate with the apicoplast-encoded ribosomal protein L4 (PfRpl4) and the large subunit rRNA to form the 50S ribosome polypeptide exit tunnel that can be occupied by azithromycin. Resistance selection experiments showed that the PfRpl22 sequence remained unchanged in azithromycin-resistant lines, while mutations in PfRpl4 altered the tunnel, implying L22's structural role in the exit tunnel but not as a direct resistance determinant.\",\n      \"method\": \"In vitro resistance selection, sequencing of resistant parasite lines, molecular modeling of the polypeptide exit tunnel\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — structural role inferred from molecular modeling and absence of mutations in L22 in resistant lines; no direct biochemical assay of L22 function performed\",\n      \"pmids\": [\"17110371\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"7G8\"},\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"Dd2\"}\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"L22 (PF3D7_0821700) was resolved as a component of the P. falciparum 80S ribosome large subunit in the first atomic-resolution cryo-EM structure of the parasite ribosome, placing it structurally within the cytoplasmic 60S ribosomal particle.\",\n      \"method\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-resolution cryo-EM structure establishes complex membership, but single study and L22 is not the focus; no mutagenesis or functional validation specific to L22\",\n      \"pmids\": [\"24913268\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"L22 (PF3D7_0821700) was incorporated into atomic models built from cryo-EM reconstructions of P. falciparum 80S ribosomes purified from blood-stage schizonts, confirming its structural presence in the large subunit of the translating ribosome.\",\n      \"method\": \"Cryo-EM reconstructions at sub-nanometer resolution with flexible fitting of atomic models from P. falciparum schizont-purified ribosomes\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — structural placement via cryo-EM atomic model, single study, no functional assay specific to L22\",\n      \"pmids\": [\"26432834\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"L22 (PF3D7_0821700) is present as a structural component of the native P. falciparum 80S ribosome in actively translating states, as visualized in situ inside infected human erythrocytes by high-resolution cryo-electron tomography.\",\n      \"method\": \"In situ cryo-electron tomography of P. falciparum-infected human erythrocytes; eight high-resolution structures of the native malarial ribosome in actively translating states\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in situ high-resolution structural data confirms ribosome membership in the native cellular context, but L22 is not individually studied functionally; single study\",\n      \"pmids\": [\"40825879\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0821700 (L22) is a structural component of the 60S large subunit of the P. falciparum cytoplasmic 80S ribosome, visualized in multiple cryo-EM and cryo-ET structures of the parasite ribosome in both isolated and native in-cell translating states; it is predicted by molecular modeling to contribute to the polypeptide exit tunnel together with PfRpl4, but no direct biochemical or mutagenesis experiments have defined a unique function for L22 beyond its ribosomal structural membership.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0821700 (L22) is a nuclear genome-encoded large-subunit ribosomal protein that serves as a structural component of the 60S large subunit of the P. falciparum cytoplasmic 80S ribosome [#1]. It has been resolved within the large subunit in successive high-resolution cryo-EM structures of the parasite ribosome purified from blood-stage schizonts [#1, #2] and visualized in situ in actively translating native ribosomes inside infected human erythrocytes by cryo-electron tomography [#3]. Molecular modeling predicts that L22 contributes together with the apicoplast-encoded PfRpl4 to the polypeptide exit tunnel that can be occupied by azithromycin, and in vitro azithromycin-resistance selection left the L22 sequence unchanged while mutations arose in PfRpl4, indicating a structural exit-tunnel role for L22 rather than a direct drug-resistance determinant [#0]. Beyond its membership in the ribosomal large subunit and its predicted exit-tunnel contribution, no direct biochemical or mutagenesis experiments defining a unique function for L22 have been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"To locate the target of azithromycin action in the parasite, resistance selection tested whether L22, predicted to line the polypeptide exit tunnel, was itself a resistance determinant, establishing L22's inferred structural role in the tunnel while excluding it as a mutational drug-resistance site.\",\n      \"evidence\": \"In vitro azithromycin resistance selection with sequencing of resistant lines and molecular modeling of the exit tunnel in P. falciparum 7G8 and Dd2\",\n      \"pmids\": [\n        \"17110371\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Structural role inferred from modeling and absence of mutations, not from direct biochemical assay of L22\",\n        \"No mutagenesis of L22 to test its exit-tunnel contribution\",\n        \"Interaction with PfRpl4 predicted, not experimentally demonstrated\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"7G8\"\n        },\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"Dd2\"\n        }\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"The first atomic-resolution cryo-EM structure of the parasite ribosome resolved where L22 sits, placing it definitively within the cytoplasmic 60S large subunit rather than in any other complex.\",\n      \"evidence\": \"Cryo-EM structure of the P. falciparum 80S ribosome at 3.2 Å resolution\",\n      \"pmids\": [\n        \"24913268\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"L22 was not the focus and received no functional validation\",\n        \"No mutagenesis linking its position to a specific translational function\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Cryo-EM reconstructions from schizont-purified ribosomes confirmed L22 as a stable structural member of the translating large subunit, reinforcing its ribosomal assignment across biological samples.\",\n      \"evidence\": \"Cryo-EM reconstructions with flexible fitting of atomic models from P. falciparum schizont-purified ribosomes\",\n      \"pmids\": [\n        \"26432834\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional assay specific to L22\",\n        \"Does not distinguish L22's role from that of neighboring large-subunit proteins\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"In situ cryo-electron tomography confirmed that L22 is a component of native, actively translating ribosomes in their cellular context, extending its structural assignment from purified particles to the intact parasite.\",\n      \"evidence\": \"In situ cryo-electron tomography of P. falciparum-infected human erythrocytes yielding eight high-resolution structures of the native ribosome in translating states\",\n      \"pmids\": [\n        \"40825879\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"L22 not individually studied functionally\",\n        \"No perturbation to test its contribution to translation in vivo\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether L22 has any function beyond structural membership in the 60S subunit — including a directly demonstrated contribution to the polypeptide exit tunnel or an interaction with PfRpl4 — remains unresolved.\",\n      \"evidence\": \"No direct biochemical or mutagenesis experiments on L22 exist in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No mutagenesis or knockdown of L22\",\n        \"No biochemical demonstration of the predicted L22–PfRpl4 exit-tunnel interaction\",\n        \"No extra-ribosomal or moonlighting role tested\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0003735\",\n        \"supporting_discovery_ids\": [1, 2, 3]\n      }\n    ],\n    \"localization\": [\n      {\n        \"term_id\": \"GO:0022625\",\n        \"supporting_discovery_ids\": [1, 2, 3]\n      },\n      {\n        \"term_id\": \"GO:0005737\",\n        \"supporting_discovery_ids\": [3]\n      }\n    ],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0006412\",\n        \"supporting_discovery_ids\": [3]\n      }\n    ],\n    \"complexes\": [\n      \"60S large ribosomal subunit of the cytoplasmic 80S ribosome\"\n    ],\n    \"partners\": [\n      \"PfRpl4 (predicted exit-tunnel co-contributor, molecular modeling only) [#0]\"\n    ],\n    \"other_free_text\": [\n      \"Predicted to contribute to the polypeptide exit tunnel occupied by azithromycin; L22 sequence unchanged in azithromycin-resistant lines, so not a direct resistance determinant [#0]\",\n      \"Structural membership established by cryo-EM (2014, 2015) and in situ cryo-ET (2025); no direct functional or mutagenesis data specific to L22 in the corpus\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_0821700","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 2 of 4 cited papers name other catalogue genes (PF3D7_0507100, PF3D7_1467400, PF3D7_0826700). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0821700","name":null,"product":"60S ribosomal protein L22, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0709100","name":null,"product":"60S ribosomal protein L22, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1315700","name":null,"product":"60S ribosomal protein L22, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}