{"gene":"PF3D7_1352400","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2022,"finding":"NUP176 (PF3D7_1352400) was identified as a component of the Plasmodium nuclear pore complex (NPC) by TurboID proximity labeling followed by affinity purification and mass spectrometry, using NUP313 as bait in P. berghei. GFP tagging confirmed its NPC localization. Gene deletion attempts indicate NUP176 is essential for parasite survival. NUP176 lacks primary sequence homology with proteins outside the Plasmodium genus.","method":"TurboID proximity labeling, affinity purification, mass spectrometry, GFP tagging (live imaging), gene deletion attempts","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proximity labeling with MS and GFP localization confirmation in a single study, single lab, two orthogonal methods (proximity labeling + GFP tagging)","pmids":["36040030"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2026,"finding":"NUP176 (PF3D7_1352400) co-purified with the P. falciparum cryptochrome-like protein PfDPL in a pulldown experiment, placing NUP176 among nuclear-pore constituents associating with PfDPL. This association suggests NUP176 may participate in nucleocytoplasmic trafficking; however, the paper only experimentally establishes co-purification and does not directly assign a mechanistic role to NUP176 itself.","method":"Co-purification/pulldown followed by mass spectrometry (PfDPL as bait)","journal":"Nature communications","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single co-purification result, single lab, no functional follow-up specific to NUP176","pmids":["41986327"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"NUP176 (PF3D7_1352400) is a Plasmodium-specific nuclear pore complex component, identified by TurboID proximity labeling and confirmed by GFP tagging at the NPC in P. berghei, where gene deletion indicates it is essential for parasite survival; it also co-purifies with the P. falciparum cryptochrome-like protein PfDPL, but no further catalytic activity or detailed mechanistic role has been established."},"narrative":{"mechanistic_narrative":"NUP176 (PF3D7_1352400) is a Plasmodium-specific constituent of the nuclear pore complex (NPC), identified by TurboID proximity labeling with the nucleoporin NUP313 as bait and confirmed at the NPC by GFP tagging in P. berghei, where deletion attempts indicate it is essential for parasite survival [PMID:36040030]. It lacks primary sequence homology to proteins outside the Plasmodium genus [PMID:36040030]. Beyond its NPC membership, no catalytic activity or detailed mechanistic role has been characterized for NUP176 in the available corpus.","teleology":[{"year":2022,"claim":"Whether PF3D7_1352400 encodes a nuclear pore component was unknown; proximity labeling from a known nucleoporin placed it at the NPC and established it as an essential, Plasmodium-restricted parasite protein.","evidence":"TurboID proximity labeling with NUP313 bait plus affinity purification/MS, GFP live imaging, and gene deletion attempts in P. berghei","pmids":["36040030"],"confidence":"Medium","gaps":["No specific molecular function or interaction interface within the NPC defined","Essentiality inferred from failed deletion rather than a conditional knockdown phenotype","Stoichiometry and position within the NPC architecture unresolved"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2026,"claim":"Whether NUP176 engages factors involved in nucleocytoplasmic trafficking was untested; co-purification with the cryptochrome-like protein PfDPL placed NUP176 among NPC constituents associating with PfDPL.","evidence":"Co-purification/pulldown with MS using PfDPL as bait in P. falciparum","pmids":["41986327"],"confidence":"Low","gaps":["Single co-purification with no NUP176-specific functional follow-up or reciprocal validation","Direct versus indirect (whole-NPC) association with PfDPL not distinguished","No mechanistic role in trafficking assigned to NUP176 itself"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The specific molecular function of NUP176 within the NPC, its direct binding partners, and its role in nucleocytoplasmic transport remain undefined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model or defined domain function","No direct interaction partners established beyond NPC co-membership","No conditional loss-of-function phenotype characterizing its essential role"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Nuclear pore complex (NPC)"],"partners":["NUP313 (PROXIMITY-LABELING BAIT)","PFDPL (CO-PURIFICATION)"],"other_free_text":["Plasmodium-specific; lacks primary sequence homology to proteins outside the Plasmodium genus [#0]","Essential for parasite survival based on failed gene deletion 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":["NUP176"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41986327","id":"","title":"GID/CTLH E3 ligase complex control cell fate programs for sexual development of Plasmodium falciparum.","date":"2026","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/41986327","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["NUP176"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4577,"output_tokens":710,"usd":0.01219,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5313,"output_tokens":1266,"usd":0.029108,"stage2_stop_reason":"end_turn"},"total_usd":0.041298,"stage1_batch_id":"msgbatch_01NE1MTa8x1hW7Lo4tAaNzY1","stage2_batch_id":"msgbatch_0141vaQdeFvbo2q39AinvXM9","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2022,\n      \"finding\": \"NUP176 (PF3D7_1352400) was identified as a component of the Plasmodium nuclear pore complex (NPC) by TurboID proximity labeling followed by affinity purification and mass spectrometry, using NUP313 as bait in P. berghei. GFP tagging confirmed its NPC localization. Gene deletion attempts indicate NUP176 is essential for parasite survival. NUP176 lacks primary sequence homology with proteins outside the Plasmodium genus.\",\n      \"method\": \"TurboID proximity labeling, affinity purification, mass spectrometry, GFP tagging (live imaging), gene deletion attempts\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proximity labeling with MS and GFP localization confirmation in a single study, single lab, two orthogonal methods (proximity labeling + GFP tagging)\",\n      \"pmids\": [\"36040030\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"NUP176 (PF3D7_1352400) co-purified with the P. falciparum cryptochrome-like protein PfDPL in a pulldown experiment, placing NUP176 among nuclear-pore constituents associating with PfDPL. This association suggests NUP176 may participate in nucleocytoplasmic trafficking; however, the paper only experimentally establishes co-purification and does not directly assign a mechanistic role to NUP176 itself.\",\n      \"method\": \"Co-purification/pulldown followed by mass spectrometry (PfDPL as bait)\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single co-purification result, single lab, no functional follow-up specific to NUP176\",\n      \"pmids\": [\"41986327\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"NUP176 (PF3D7_1352400) is a Plasmodium-specific nuclear pore complex component, identified by TurboID proximity labeling and confirmed by GFP tagging at the NPC in P. berghei, where gene deletion indicates it is essential for parasite survival; it also co-purifies with the P. falciparum cryptochrome-like protein PfDPL, but no further catalytic activity or detailed mechanistic role has been established.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NUP176 (PF3D7_1352400) is a Plasmodium-specific constituent of the nuclear pore complex (NPC), identified by TurboID proximity labeling with the nucleoporin NUP313 as bait and confirmed at the NPC by GFP tagging in P. berghei, where deletion attempts indicate it is essential for parasite survival [#0]. It lacks primary sequence homology to proteins outside the Plasmodium genus [#0]. Beyond its NPC membership, no catalytic activity or detailed mechanistic role has been characterized for NUP176 in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"Whether PF3D7_1352400 encodes a nuclear pore component was unknown; proximity labeling from a known nucleoporin placed it at the NPC and established it as an essential, Plasmodium-restricted parasite protein.\",\n      \"evidence\": \"TurboID proximity labeling with NUP313 bait plus affinity purification/MS, GFP live imaging, and gene deletion attempts in P. berghei\",\n      \"pmids\": [\"36040030\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No specific molecular function or interaction interface within the NPC defined\",\n        \"Essentiality inferred from failed deletion rather than a conditional knockdown phenotype\",\n        \"Stoichiometry and position within the NPC architecture unresolved\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Whether NUP176 engages factors involved in nucleocytoplasmic trafficking was untested; co-purification with the cryptochrome-like protein PfDPL placed NUP176 among NPC constituents associating with PfDPL.\",\n      \"evidence\": \"Co-purification/pulldown with MS using PfDPL as bait in P. falciparum\",\n      \"pmids\": [\"41986327\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single co-purification with no NUP176-specific functional follow-up or reciprocal validation\",\n        \"Direct versus indirect (whole-NPC) association with PfDPL not distinguished\",\n        \"No mechanistic role in trafficking assigned to NUP176 itself\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The specific molecular function of NUP176 within the NPC, its direct binding partners, and its role in nucleocytoplasmic transport remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural model or defined domain function\",\n        \"No direct interaction partners established beyond NPC co-membership\",\n        \"No conditional loss-of-function phenotype characterizing its essential role\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005643\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [\"Nuclear pore complex (NPC)\"],\n    \"partners\": [\"NUP313 (proximity-labeling bait)\", \"PfDPL (co-purification)\"],\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 failed gene deletion in P. berghei [#0]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1352400","name":null,"product":"nucleoporin NUP176, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1365100","name":null,"product":"conserved Plasmodium protein, unknown function","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1248600","name":null,"product":"nucleoporin NUP176, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"NUP176","evaluation":null}