{"gene":"PF3D7_0212500","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":2022,"finding":"NUP434 (PF3D7_0212500) was identified as a component of the Plasmodium nuclear pore complex (NPC) by TurboID proximity labeling followed by affinity purification and mass spectrometry, and confirmed by GFP tagging; gene deletion attempts indicate NUP434 is essential to parasite survival.","method":"TurboID proximity labeling, affinity purification, mass spectrometry, GFP tagging, gene deletion","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proximity labeling plus MS identification, confirmed by GFP localization, and essentiality supported by failed deletion; single lab, multiple orthogonal methods but no full mechanistic dissection of NUP434's molecular function.","pmids":["36040030"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"NUP434 (PF3D7_0212500) is a Plasmodium-specific nuclear pore complex component, identified by proximity labeling and confirmed by GFP tagging, that lacks primary sequence homology outside the Plasmodium genus and is essential for parasite survival, but its precise molecular function within the NPC remains uncharacterized."},"narrative":{"mechanistic_narrative":"NUP434 (PF3D7_0212500) is a component of the Plasmodium nuclear pore complex (NPC), identified by TurboID proximity labeling coupled to affinity purification and mass spectrometry and confirmed by GFP tagging, with failed gene deletion indicating it is essential for parasite survival [PMID:36040030]. Beyond its assignment to the NPC and its essentiality, no further mechanistic detail—including its precise molecular function, its interactions with specific nucleoporins, or its structural role within the pore—has been characterized in the available corpus.","teleology":[{"year":2022,"claim":"Whether PF3D7_0212500 is a bona fide constituent of the parasite nuclear pore and whether it matters for viability was unknown; proximity labeling placed it at the NPC and deletion attempts established that it is required for survival.","evidence":"TurboID proximity labeling, affinity purification and mass spectrometry, GFP tagging, and gene deletion in Plasmodium berghei","pmids":["36040030"],"confidence":"Medium","gaps":["The specific molecular function of NUP434 within the NPC is not defined","Direct binding partners or subcomplex membership among nucleoporins are not resolved","Essentiality is inferred from failed deletion rather than a conditional knockdown demonstrating the terminal phenotype"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"The precise molecular role of NUP434 within the nuclear pore—its structural position, direct interactors, and the cellular process it enables—remains to be determined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No mechanistic dissection of NUP434 function beyond NPC association","No structural model or defined subcomplex placement","No conditional depletion linking NUP434 loss to a specific defect"],"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Plasmodium nuclear pore complex (NPC)"],"partners":[],"other_free_text":["Identified as an NPC component by TurboID proximity labeling and confirmed by GFP tagging [#0]","Essential for parasite survival based on failed gene deletion [#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":375,"usd":0.008229,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4874,"output_tokens":976,"usd":0.024385,"stage2_stop_reason":"end_turn"},"total_usd":0.032614,"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\": \"NUP434 (PF3D7_0212500) was identified as a component of the Plasmodium nuclear pore complex (NPC) by TurboID proximity labeling followed by affinity purification and mass spectrometry, and confirmed by GFP tagging; gene deletion attempts indicate NUP434 is essential to parasite survival.\",\n      \"method\": \"TurboID proximity labeling, affinity purification, mass spectrometry, GFP tagging, gene deletion\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proximity labeling plus MS identification, confirmed by GFP localization, and essentiality supported by failed deletion; single lab, multiple orthogonal methods but no full mechanistic dissection of NUP434's molecular function.\",\n      \"pmids\": [\"36040030\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"NUP434 (PF3D7_0212500) is a Plasmodium-specific nuclear pore complex component, identified by proximity labeling and confirmed by GFP tagging, that lacks primary sequence homology outside the Plasmodium genus and is essential for parasite survival, but its precise molecular function within the NPC remains uncharacterized.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NUP434 (PF3D7_0212500) is a component of the Plasmodium nuclear pore complex (NPC), identified by TurboID proximity labeling coupled to affinity purification and mass spectrometry and confirmed by GFP tagging, with failed gene deletion indicating it is essential for parasite survival [#0]. Beyond its assignment to the NPC and its essentiality, no further mechanistic detail—including its precise molecular function, its interactions with specific nucleoporins, or its structural role within the pore—has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"Whether PF3D7_0212500 is a bona fide constituent of the parasite nuclear pore and whether it matters for viability was unknown; proximity labeling placed it at the NPC and deletion attempts established that it is required for survival.\",\n      \"evidence\": \"TurboID proximity labeling, affinity purification and mass spectrometry, GFP tagging, and gene deletion in Plasmodium berghei\",\n      \"pmids\": [\"36040030\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The specific molecular function of NUP434 within the NPC is not defined\",\n        \"Direct binding partners or subcomplex membership among nucleoporins are not resolved\",\n        \"Essentiality is inferred from failed deletion rather than a conditional knockdown demonstrating the terminal phenotype\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium berghei\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The precise molecular role of NUP434 within the nuclear pore—its structural position, direct interactors, and the cellular process it enables—remains to be determined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No mechanistic dissection of NUP434 function beyond NPC association\",\n        \"No structural model or defined subcomplex placement\",\n        \"No conditional depletion linking NUP434 loss to a specific defect\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium berghei\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005643\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [\"Plasmodium nuclear pore complex (NPC)\"],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Identified as an NPC component by TurboID proximity labeling and confirmed by GFP tagging [#0]\",\n      \"Essential for parasite survival based on failed gene deletion [#0]\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_0212500","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_0212500","name":null,"product":"nucleoporin NUP434, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0309400","name":null,"product":"conserved Plasmodium protein, unknown function","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0408700","name":null,"product":"nucleoporin NUP434, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"NUP434","evaluation":null}