{"gene":"TG_310470","gene_symbol":"COX2b","run_date":"2026-09-08T15:15:13","timeline":{"discoveries":[{"year":2007,"finding":"COX2B (together with COX2A) is an essential subunit of the mitochondrial cytochrome c oxidase (Complex IV) in Toxoplasma gondii, localizing to the mitochondria and co-migrating with Complex IV on Blue Native/2D electrophoresis.","method":"Immunochemical localization with anti-recombinant COX2B antibody, mitochondrial fractionation, Blue Native PAGE followed by 2D electrophoresis, mass spectrometry identification, and cyanide-sensitive oxygen uptake assay of mitochondria-enriched fractions.","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization with functional fractionation and co-migration with Complex IV confirmed by MS; single lab, multiple orthogonal methods but no genetic loss-of-function.","pmids":["18036550"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"COX2B is a nuclear-encoded subunit of the mitochondrial cytochrome c oxidase (Complex IV) in Toxoplasma gondii, localizing to the parasite's mitochondria and associating with the functional respiratory complex."},"narrative":{"mechanistic_narrative":"COX2b is a nuclear-encoded subunit of the mitochondrial cytochrome c oxidase (Complex IV) in Toxoplasma gondii, where it localizes to the parasite mitochondria and, together with COX2A, co-migrates with the assembled Complex IV on Blue Native/2D electrophoresis and is identified in that complex by mass spectrometry [PMID:18036550]. Mitochondria-enriched fractions containing this complex support cyanide-sensitive oxygen uptake, placing COX2b within the functional respiratory chain [PMID:18036550]. Beyond this localization and complex-association evidence, no further mechanistic detail — including genetic loss-of-function characterization — has been established in the available corpus.","teleology":[{"year":2007,"claim":"The question of which subunits constitute Toxoplasma Complex IV was addressed by showing COX2B is a mitochondrial subunit that physically associates with the assembled, respiration-competent enzyme.","evidence":"Anti-recombinant COX2B antibody immunolocalization, mitochondrial fractionation, Blue Native PAGE with 2D electrophoresis, MS identification, and cyanide-sensitive oxygen uptake assay","pmids":["18036550"],"confidence":"Medium","gaps":["No genetic loss-of-function to demonstrate that COX2B is required for Complex IV assembly or activity","The molecular role of COX2B within the complex (e.g. catalytic contribution, structural stabilization) is not defined","The relationship between COX2A and COX2B, and why the subunit is split, is not resolved"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"Whether COX2B is functionally essential and its specific mechanistic contribution to Complex IV catalysis remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No conditional knockout or knockdown phenotype","No structural model of the T. gondii Complex IV incorporating COX2B","Import and assembly pathway of the nuclear-encoded subunit not characterized"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Mitochondrial cytochrome c oxidase (Complex IV)"],"partners":["COX2A"],"other_free_text":["Nuclear-encoded subunit imported into the parasite mitochondrion; co-migrates with Complex IV and is associated with cyanide-sensitive oxygen uptake activity."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"18036550","id":"PMC_18036550","title":"The polypeptides COX2A and COX2B are essential components of the mitochondrial cytochrome c oxidase of Toxoplasma gondii.","date":"2007","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/18036550","citation_count":8,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2986,"output_tokens":371,"usd":0.007261,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4980,"output_tokens":1245,"usd":0.028012,"stage2_stop_reason":"end_turn"},"total_usd":0.035273,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"COX2B (together with COX2A) is an essential subunit of the mitochondrial cytochrome c oxidase (Complex IV) in Toxoplasma gondii, localizing to the mitochondria and co-migrating with Complex IV on Blue Native/2D electrophoresis.\",\n      \"method\": \"Immunochemical localization with anti-recombinant COX2B antibody, mitochondrial fractionation, Blue Native PAGE followed by 2D electrophoresis, mass spectrometry identification, and cyanide-sensitive oxygen uptake assay of mitochondria-enriched fractions.\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization with functional fractionation and co-migration with Complex IV confirmed by MS; single lab, multiple orthogonal methods but no genetic loss-of-function.\",\n      \"pmids\": [\"18036550\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"COX2B is a nuclear-encoded subunit of the mitochondrial cytochrome c oxidase (Complex IV) in Toxoplasma gondii, localizing to the parasite's mitochondria and associating with the functional respiratory complex.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"COX2b is a nuclear-encoded subunit of the mitochondrial cytochrome c oxidase (Complex IV) in Toxoplasma gondii, where it localizes to the parasite mitochondria and, together with COX2A, co-migrates with the assembled Complex IV on Blue Native/2D electrophoresis and is identified in that complex by mass spectrometry [#0]. Mitochondria-enriched fractions containing this complex support cyanide-sensitive oxygen uptake, placing COX2b within the functional respiratory chain [#0]. Beyond this localization and complex-association evidence, no further mechanistic detail — including genetic loss-of-function characterization — has been established in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"The question of which subunits constitute Toxoplasma Complex IV was addressed by showing COX2B is a mitochondrial subunit that physically associates with the assembled, respiration-competent enzyme.\",\n      \"evidence\": \"Anti-recombinant COX2B antibody immunolocalization, mitochondrial fractionation, Blue Native PAGE with 2D electrophoresis, MS identification, and cyanide-sensitive oxygen uptake assay\",\n      \"pmids\": [\"18036550\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No genetic loss-of-function to demonstrate that COX2B is required for Complex IV assembly or activity\",\n        \"The molecular role of COX2B within the complex (e.g. catalytic contribution, structural stabilization) is not defined\",\n        \"The relationship between COX2A and COX2B, and why the subunit is split, is not resolved\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether COX2B is functionally essential and its specific mechanistic contribution to Complex IV catalysis remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No conditional knockout or knockdown phenotype\",\n        \"No structural model of the T. gondii Complex IV incorporating COX2B\",\n        \"Import and assembly pathway of the nuclear-encoded subunit not characterized\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004129\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006119\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\n      \"Mitochondrial cytochrome c oxidase (Complex IV)\"\n    ],\n    \"partners\": [\n      \"COX2A\"\n    ],\n    \"other_free_text\": [\n      \"Nuclear-encoded subunit imported into the parasite mitochondrion; co-migrates with Complex IV and is associated with cyanide-sensitive oxygen uptake activity.\"\n    ]\n  },\n  \"strain_conflicts\": []\n}\n```","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_310470","name":"COX2b","product":"cytochrome c oxidase subunit COX2b","uniprot_acc":"A0A125YMT5","chromosome":"TGME49_chrXI","start_pos":1375316},{"strain":"GT1","gene_id":"TGGT1_310470","name":null,"product":"putative cytochrome C oxidase subunit IIb","uniprot_acc":null,"chromosome":"TGGT1_chrXI","start_pos":1338649},{"strain":"RH88","gene_id":"TGRH88_050010","name":null,"product":"putative cytochrome C oxidase subunit IIb","uniprot_acc":null,"chromosome":"CM023092","start_pos":1424427},{"strain":"VEG","gene_id":"TGVEG_310470","name":null,"product":"putative cytochrome C oxidase subunit IIb","uniprot_acc":"A0A0F7V9B5","chromosome":"TGVEG_chrXI","start_pos":1387288}]}