{"gene":"TG_313480","gene_symbol":"AAP3","run_date":"2026-09-10T21:09:19","timeline":{"discoveries":[{"year":2019,"finding":"AAP3 (along with AAP1, AAP2, AAP4, AAP5, Centrin2, and an apical annuli methyltransferase) was identified as a component of the apical annuli of Toxoplasma gondii, structures embedded within the inner membrane complex (IMC) sutures, validated by reciprocal proximity biotinylation (BioID).","method":"Reciprocal BioID proximity biotinylation proteome mapping; super-resolution microscopy","journal":"Cellular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal BioID with super-resolution microscopy validation in a single study; robust but single-lab, no in vitro reconstitution or mutagenesis","pmids":["31470470"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"The apical annuli complex, of which AAP3 is a member, is organized in a concentric four-ring structure with diameters ranging from 200 to 400 nm, as revealed by super-resolution microscopy.","method":"Super-resolution microscopy","journal":"Cellular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct super-resolution imaging of the structure, single lab, single method","pmids":["31470470"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"finding":"AAP3, as part of the apical annuli proteins, carries domain signatures shared with centrosomal proteins (coiled-coil and signalling domains), and phylogenetic analysis showed that the AAPs are conserved narrowly in coccidian apicomplexan parasites that multiply by internal budding, suggesting a role linked to internal budding replication.","method":"Phylogenetic analysis; domain signature analysis","journal":"Cellular microbiology","confidence":"Low","confidence_rationale":"Tier 4 / Weak — based on computational/comparative analysis only, no direct functional experiment for AAP3 specifically","pmids":["31470470"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"AAP3 is a coiled-coil and signalling domain-containing protein localized to the apical annuli of Toxoplasma gondii, where it resides within the inner membrane complex sutures as part of a multi-protein complex (AAP1–5, Centrin2, and an apical annuli methyltransferase) organized in a concentric four-ring pore-like structure, conserved among coccidian apicomplexans that replicate by internal budding."},"narrative":{"mechanistic_narrative":"AAP3 is a component of the apical annuli of Toxoplasma gondii, structures embedded within the sutures of the inner membrane complex (IMC), where it resides together with AAP1, AAP2, AAP4, AAP5, Centrin2, and an apical annuli methyltransferase as identified by reciprocal proximity biotinylation (BioID) and validated by super-resolution microscopy [PMID:31470470]. Within this compartment, the apical annuli complex is organized as a concentric four-ring, pore-like structure of 200–400 nm diameter [PMID:31470470]. Beyond its identification as an apical annuli complex member and its localization, no further mechanistic detail about AAP3 has been characterized in the available corpus.","teleology":[{"year":2019,"claim":"Establishing that the apical annuli of Toxoplasma have a defined protein composition answered what molecules build these IMC-suture structures, placing AAP3 within a discrete multi-protein complex.","evidence":"Reciprocal BioID proximity biotinylation proteome mapping with super-resolution microscopy validation in Toxoplasma gondii","pmids":["31470470"],"confidence":"Medium","gaps":["No mutagenesis or knockout to establish AAP3's functional role","Direct binding partners of AAP3 within the complex not resolved","No in vitro reconstitution of the complex"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"claim":"Super-resolution imaging resolved the architecture of the AAP3-containing apical annuli as a concentric four-ring pore-like structure, defining its spatial organization.","evidence":"Super-resolution microscopy of Toxoplasma gondii apical annuli","pmids":["31470470"],"confidence":"Medium","gaps":["Position of AAP3 within the four-ring architecture not resolved","Functional consequence of the ring geometry unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2019,"claim":"Comparative and domain analysis linked AAPs, including AAP3, to centrosomal-type coiled-coil/signalling domains and to coccidian parasites replicating by internal budding, hinting at a role tied to that replication mode.","evidence":"Phylogenetic and domain signature analysis of the apical annuli proteins","pmids":["31470470"],"confidence":"Low","gaps":["Inference is computational only, with no direct functional experiment for AAP3","The proposed link to internal budding replication is untested","Signalling activity of the predicted domains not demonstrated"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Apical annuli complex (AAP1, AAP2, AAP3, AAP4, AAP5, Centrin2, apical annuli methyltransferase)"],"partners":["AAP1","AAP2","AAP4","AAP5","CENTRIN2","APICAL ANNULI METHYLTRANSFERASE"],"other_free_text":["Apical annuli organized as a concentric four-ring pore-like structure, 200-400 nm diameter [#1]","Carries coiled-coil and signalling domain signatures shared with centrosomal proteins; conserved narrowly in coccidian apicomplexans replicating by internal budding [#2]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"31470470","id":"PMC_31470470","title":"The apical annuli of Toxoplasma gondii are composed of coiled-coil and signalling proteins embedded in the inner membrane complex sutures.","date":"2019","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/31470470","citation_count":38,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2950,"output_tokens":593,"usd":0.008873,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5278,"output_tokens":1291,"usd":0.029333,"stage2_stop_reason":"end_turn"},"total_usd":0.085435,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","note":"batch pricing = 50% of standard","corrective_rerun":"2026-09-10 wrong-gene rerun (round-4 rules)","corrective_reason":"re-read with subject anchor"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"AAP3 (along with AAP1, AAP2, AAP4, AAP5, Centrin2, and an apical annuli methyltransferase) was identified as a component of the apical annuli of Toxoplasma gondii, structures embedded within the inner membrane complex (IMC) sutures, validated by reciprocal proximity biotinylation (BioID).\",\n      \"method\": \"Reciprocal BioID proximity biotinylation proteome mapping; super-resolution microscopy\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal BioID with super-resolution microscopy validation in a single study; robust but single-lab, no in vitro reconstitution or mutagenesis\",\n      \"pmids\": [\"31470470\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The apical annuli complex, of which AAP3 is a member, is organized in a concentric four-ring structure with diameters ranging from 200 to 400 nm, as revealed by super-resolution microscopy.\",\n      \"method\": \"Super-resolution microscopy\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct super-resolution imaging of the structure, single lab, single method\",\n      \"pmids\": [\"31470470\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"AAP3, as part of the apical annuli proteins, carries domain signatures shared with centrosomal proteins (coiled-coil and signalling domains), and phylogenetic analysis showed that the AAPs are conserved narrowly in coccidian apicomplexan parasites that multiply by internal budding, suggesting a role linked to internal budding replication.\",\n      \"method\": \"Phylogenetic analysis; domain signature analysis\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — based on computational/comparative analysis only, no direct functional experiment for AAP3 specifically\",\n      \"pmids\": [\"31470470\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"AAP3 is a coiled-coil and signalling domain-containing protein localized to the apical annuli of Toxoplasma gondii, where it resides within the inner membrane complex sutures as part of a multi-protein complex (AAP1–5, Centrin2, and an apical annuli methyltransferase) organized in a concentric four-ring pore-like structure, conserved among coccidian apicomplexans that replicate by internal budding.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"AAP3 is a component of the apical annuli of Toxoplasma gondii, structures embedded within the sutures of the inner membrane complex (IMC), where it resides together with AAP1, AAP2, AAP4, AAP5, Centrin2, and an apical annuli methyltransferase as identified by reciprocal proximity biotinylation (BioID) and validated by super-resolution microscopy [#0]. Within this compartment, the apical annuli complex is organized as a concentric four-ring, pore-like structure of 200\\u2013400 nm diameter [#1]. Beyond its identification as an apical annuli complex member and its localization, no further mechanistic detail about AAP3 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Establishing that the apical annuli of Toxoplasma have a defined protein composition answered what molecules build these IMC-suture structures, placing AAP3 within a discrete multi-protein complex.\",\n      \"evidence\": \"Reciprocal BioID proximity biotinylation proteome mapping with super-resolution microscopy validation in Toxoplasma gondii\",\n      \"pmids\": [\n        \"31470470\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No mutagenesis or knockout to establish AAP3's functional role\",\n        \"Direct binding partners of AAP3 within the complex not resolved\",\n        \"No in vitro reconstitution of the complex\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Super-resolution imaging resolved the architecture of the AAP3-containing apical annuli as a concentric four-ring pore-like structure, defining its spatial organization.\",\n      \"evidence\": \"Super-resolution microscopy of Toxoplasma gondii apical annuli\",\n      \"pmids\": [\n        \"31470470\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Position of AAP3 within the four-ring architecture not resolved\",\n        \"Functional consequence of the ring geometry unknown\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Comparative and domain analysis linked AAPs, including AAP3, to centrosomal-type coiled-coil/signalling domains and to coccidian parasites replicating by internal budding, hinting at a role tied to that replication mode.\",\n      \"evidence\": \"Phylogenetic and domain signature analysis of the apical annuli proteins\",\n      \"pmids\": [\n        \"31470470\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Inference is computational only, with no direct functional experiment for AAP3\",\n        \"The proposed link to internal budding replication is untested\",\n        \"Signalling activity of the predicted domains not demonstrated\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular function of AAP3 and its specific contribution to apical annuli assembly or parasite replication remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No loss-of-function phenotype for AAP3\",\n        \"No direct binding partner or structural placement within the complex\",\n        \"No demonstrated biochemical activity\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Toxoplasma gondii\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\n        \"term_id\": \"apical annuli (inner membrane complex sutures)\",\n        \"supporting_discovery_ids\": [\n          0,\n          1\n        ],\n        \"attribution\": [\n          {\n            \"species\": \"Toxoplasma gondii\",\n            \"strain\": \"\"\n          }\n        ]\n      }\n    ],\n    \"pathway\": [],\n    \"complexes\": [\n      \"Apical annuli complex (AAP1, AAP2, AAP3, AAP4, AAP5, Centrin2, apical annuli methyltransferase)\"\n    ],\n    \"partners\": [\n      \"AAP1\",\n      \"AAP2\",\n      \"AAP4\",\n      \"AAP5\",\n      \"Centrin2\",\n      \"apical annuli methyltransferase\"\n    ],\n    \"other_free_text\": [\n      \"Apical annuli organized as a concentric four-ring pore-like structure, 200-400 nm diameter [#1]\",\n      \"Carries coiled-coil and signalling domain signatures shared with centrosomal proteins; conserved narrowly in coccidian apicomplexans replicating by internal budding [#2]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_313480","name":"AAP3","product":"apical annuli protein AAP3","uniprot_acc":"S8ERD7","chromosome":"TGME49_chrXI","start_pos":3422220},{"strain":"GT1","gene_id":"TGGT1_313480","name":null,"product":"hypothetical protein","uniprot_acc":null,"chromosome":"TGGT1_chrXI","start_pos":3385333},{"strain":"RH88","gene_id":"TGRH88_052640","name":null,"product":"unspecified product","uniprot_acc":null,"chromosome":"CM023092","start_pos":3471062},{"strain":"VEG","gene_id":"TGVEG_313480","name":null,"product":"hypothetical protein","uniprot_acc":"A0A125YII9","chromosome":"TGVEG_chrXI","start_pos":3435510}]}