{"gene":"PF3D7_0212400","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":2022,"finding":"NUP390 (PF3D7_0212400) was identified as a component of the Plasmodium nuclear pore complex (NPC) by TurboID proximity labeling followed by affinity purification and mass spectrometry, with NPC localization confirmed by GFP tagging. Gene deletion attempts indicate NUP390 is essential for parasite survival. NUP390 lacks primary sequence homology with proteins outside the Plasmodium genus.","method":"TurboID proximity labeling, affinity purification, mass spectrometry, GFP tagging, gene deletion attempts","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proximity labeling with MS identification plus GFP localization confirmation and gene-deletion essentiality data, single lab study","pmids":["36040030"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"NUP390 (PF3D7_0212400) is a Plasmodium-specific nucleoporin that localizes to the nuclear pore complex and is essential for parasite survival, identified by TurboID proximity labeling and confirmed by GFP tagging in P. berghei, but its precise molecular function within the NPC remains uncharacterized."},"narrative":{"mechanistic_narrative":"NUP390 (PF3D7_0212400) is a Plasmodium-specific nucleoporin that is a component of the parasite nuclear pore complex (NPC), identified by TurboID proximity labeling with affinity purification and mass spectrometry and confirmed to localize to the NPC by GFP tagging in P. berghei [PMID:36040030]. Gene deletion attempts indicate NUP390 is essential for parasite survival, and the protein lacks primary sequence homology to proteins outside the Plasmodium genus [PMID:36040030]. Beyond its identification as an essential NPC component [PMID:36040030], no further mechanistic detail — including its specific molecular function, interacting substructures within the NPC, or role in nucleocytoplasmic transport — has been characterized in the available corpus.","teleology":[{"year":2022,"claim":"Whether PF3D7_0212400 belongs to the parasite nuclear pore complex was unknown; proximity labeling and imaging established it as an essential, Plasmodium-specific nucleoporin.","evidence":"TurboID proximity labeling with affinity purification and mass spectrometry, GFP tagging for localization, and gene deletion attempts in P. berghei","pmids":["36040030"],"confidence":"Medium","gaps":["The precise molecular function of NUP390 within the NPC is not defined","Direct binding partners and NPC substructure assignment are not established","Essentiality is inferred from failed deletion attempts rather than a conditional knockdown mechanistic study"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"The specific molecular role of NUP390 in nuclear pore assembly, nucleocytoplasmic transport, or other NPC-associated processes remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No functional assay linking NUP390 to a specific NPC activity","No structural model or sub-complex assignment","No characterization of how loss of NUP390 impairs parasite survival at the molecular level"],"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["nuclear pore complex (NPC)"],"partners":[],"other_free_text":["Plasmodium-specific; lacks primary sequence homology to proteins outside the Plasmodium genus [#0]","Essential for parasite survival based on gene deletion attempts [#0]","Identified by TurboID proximity labeling and confirmed by GFP tagging in P. berghei [#0]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"36040030","id":"PMC_36040030","title":"TurboID Identification of Evolutionarily Divergent Components of the Nuclear Pore Complex in the Malaria Model Plasmodium berghei.","date":"2022","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/36040030","citation_count":14,"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":3611,"output_tokens":382,"usd":0.008282,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4877,"output_tokens":1110,"usd":0.026068,"stage2_stop_reason":"end_turn"},"total_usd":0.03435,"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\": 2022,\n      \"finding\": \"NUP390 (PF3D7_0212400) was identified as a component of the Plasmodium nuclear pore complex (NPC) by TurboID proximity labeling followed by affinity purification and mass spectrometry, with NPC localization confirmed by GFP tagging. Gene deletion attempts indicate NUP390 is essential for parasite survival. NUP390 lacks primary sequence homology with proteins outside the Plasmodium genus.\",\n      \"method\": \"TurboID proximity labeling, affinity purification, mass spectrometry, GFP tagging, gene deletion attempts\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proximity labeling with MS identification plus GFP localization confirmation and gene-deletion essentiality data, single lab study\",\n      \"pmids\": [\"36040030\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"NUP390 (PF3D7_0212400) is a Plasmodium-specific nucleoporin that localizes to the nuclear pore complex and is essential for parasite survival, identified by TurboID proximity labeling and confirmed by GFP tagging in P. berghei, but its precise molecular function within the NPC remains uncharacterized.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"NUP390 (PF3D7_0212400) is a Plasmodium-specific nucleoporin that is a component of the parasite nuclear pore complex (NPC), identified by TurboID proximity labeling with affinity purification and mass spectrometry and confirmed to localize to the NPC by GFP tagging in P. berghei [#0]. Gene deletion attempts indicate NUP390 is essential for parasite survival, and the protein lacks primary sequence homology to proteins outside the Plasmodium genus [#0]. Beyond its identification as an essential NPC component [#0], no further mechanistic detail — including its specific molecular function, interacting substructures within the NPC, or role in nucleocytoplasmic transport — has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"Whether PF3D7_0212400 belongs to the parasite nuclear pore complex was unknown; proximity labeling and imaging established it as an essential, Plasmodium-specific nucleoporin.\",\n      \"evidence\": \"TurboID proximity labeling with affinity purification and mass spectrometry, GFP tagging for localization, and gene deletion attempts in P. berghei\",\n      \"pmids\": [\"36040030\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The precise molecular function of NUP390 within the NPC is not defined\",\n        \"Direct binding partners and NPC substructure assignment are not established\",\n        \"Essentiality is inferred from failed deletion attempts rather than a conditional knockdown mechanistic study\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium berghei\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The specific molecular role of NUP390 in nuclear pore assembly, nucleocytoplasmic transport, or other NPC-associated processes remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional assay linking NUP390 to a specific NPC activity\",\n        \"No structural model or sub-complex assignment\",\n        \"No characterization of how loss of NUP390 impairs parasite survival at the molecular level\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium berghei\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0017056\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005643\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [\"nuclear pore complex (NPC)\"],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Plasmodium-specific; lacks primary sequence homology to proteins outside the Plasmodium genus [#0]\",\n      \"Essential for parasite survival based on gene deletion attempts [#0]\",\n      \"Identified by TurboID proximity labeling and confirmed by GFP tagging in P. berghei [#0]\"\n    ]\n  }\n}\n```","audit_flag":{"gene":"PF3D7_0212400","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 1 of 1 cited papers name other catalogue genes (PF3D7_0609000, PF3D7_1352400). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0212400","name":null,"product":"nucleoporin NUP390, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0309200","name":null,"product":"conserved Plasmodium protein, unknown function","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0408800","name":null,"product":"nucleoporin NUP390, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"NUP390","evaluation":null}