{"gene":"PF3D7_1473900","run_date":"2026-09-08T15:24:04","timeline":{"discoveries":[{"year":2022,"finding":"NUF1P1 (NUFIP1, PF3D7_1473900) from P. falciparum forms a thermally stable, species-dependent complex with ZNHIT3; the three-dimensional structure of this complex was solved, revealing key hydrophobic residues at the interaction interface. The free ZNHIT3 fragment that binds NUF1P1 was shown to multimerize in vitro and to adopt conformational changes that bury the hydrophobic residues required for NUF1P1 binding.","method":"X-ray crystallography / structural determination of the ZNHIT3–NUFIP1 complex, in vitro biochemical characterization (multimerization assay), and comparison with AlphaFold predictions","journal":"Biochemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — crystal structure of the complex determined, but single lab and single study; functional validation in the parasite is absent","pmids":["35315277"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"NUF1P1 (PF3D7_1473900) is a P. falciparum ribosome-assembly protein whose structure has been determined as part of a species-dependent complex with ZNHIT3, with key hydrophobic residues mediating the interaction interface, linking it to ribosomal RNA modification and ribophagy pathways; no further in-parasite mechanistic data are available."},"narrative":{"mechanistic_narrative":"NUF1P1 (PF3D7_1473900) is a Plasmodium falciparum protein implicated in ribosome assembly that has been characterized structurally through its interaction with ZNHIT3 [PMID:35315277]. X-ray crystallography of the ZNHIT3–NUF1P1 complex revealed a thermally stable, species-dependent assembly in which key hydrophobic residues form the interaction interface; the ZNHIT3 fragment that engages NUF1P1 can multimerize in vitro and undergoes conformational changes that bury the hydrophobic residues required for NUF1P1 binding, regulating complex formation [PMID:35315277]. Beyond this structural characterization of the ZNHIT3–NUF1P1 interface [PMID:35315277], no further in-parasite mechanistic detail — including functional validation, substrate engagement, or subcellular localization of NUF1P1 — has been characterized in the available corpus.","teleology":[{"year":2022,"claim":"To establish how P. falciparum NUF1P1 engages its partner ZNHIT3, this study asked what the physical basis of the interaction is and resolved the atomic structure of the complex.","evidence":"X-ray crystallography of the ZNHIT3–NUF1P1 complex with in vitro multimerization assays and AlphaFold comparison, in P. falciparum","pmids":["35315277"],"confidence":"Medium","gaps":["No functional validation of NUF1P1 in the parasite; the biological consequence of the interaction is untested","The precise role of NUF1P1 in ribosome assembly or rRNA modification is not experimentally demonstrated here","Single lab, single study without independent confirmation"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether NUF1P1 functions in ribosome assembly, rRNA modification, or related pathways in the living parasite remains unestablished.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No in-parasite loss-of-function or localization data for NUF1P1","No identified substrate or downstream effector","No demonstration that the ZNHIT3 interaction is required for a specific cellular process"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["ZNHIT3–NUF1P1 complex (PF3D7_1473900 with ZNHIT3)"],"partners":["ZNHIT3"],"other_free_text":["The ZNHIT3–NUF1P1 interaction is species-dependent and thermally stable, mediated by hydrophobic interface residues [#0].","The free ZNHIT3 fragment multimerizes in vitro and adopts conformations that bury the residues required for NUF1P1 binding [#0]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"35315277","id":"PMC_35315277","title":"Structural Analysis of the Plasmodial Proteins ZNHIT3 and NUFIP1 Provides Insights into the Selectivity of a Conserved Interaction.","date":"2022","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/35315277","citation_count":5,"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":3298,"output_tokens":431,"usd":0.008179,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4933,"output_tokens":1180,"usd":0.027082,"stage2_stop_reason":"end_turn"},"total_usd":0.035261,"stage1_batch_id":"msgbatch_01S4WrhSkksYHeZXxqf3za3o","stage2_batch_id":"msgbatch_019VBBeuW6G52X8gZfsFDfb5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2022,\n      \"finding\": \"NUF1P1 (NUFIP1, PF3D7_1473900) from P. falciparum forms a thermally stable, species-dependent complex with ZNHIT3; the three-dimensional structure of this complex was solved, revealing key hydrophobic residues at the interaction interface. The free ZNHIT3 fragment that binds NUF1P1 was shown to multimerize in vitro and to adopt conformational changes that bury the hydrophobic residues required for NUF1P1 binding.\",\n      \"method\": \"X-ray crystallography / structural determination of the ZNHIT3–NUFIP1 complex, in vitro biochemical characterization (multimerization assay), and comparison with AlphaFold predictions\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — crystal structure of the complex determined, but single lab and single study; functional validation in the parasite is absent\",\n      \"pmids\": [\"35315277\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"NUF1P1 (PF3D7_1473900) is a P. falciparum ribosome-assembly protein whose structure has been determined as part of a species-dependent complex with ZNHIT3, with key hydrophobic residues mediating the interaction interface, linking it to ribosomal RNA modification and ribophagy pathways; no further in-parasite mechanistic data are available.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NUF1P1 (PF3D7_1473900) is a Plasmodium falciparum protein implicated in ribosome assembly that has been characterized structurally through its interaction with ZNHIT3 [#0]. X-ray crystallography of the ZNHIT3–NUF1P1 complex revealed a thermally stable, species-dependent assembly in which key hydrophobic residues form the interaction interface; the ZNHIT3 fragment that engages NUF1P1 can multimerize in vitro and undergoes conformational changes that bury the hydrophobic residues required for NUF1P1 binding, regulating complex formation [#0]. Beyond this structural characterization of the ZNHIT3–NUF1P1 interface [#0], no further in-parasite mechanistic detail — including functional validation, substrate engagement, or subcellular localization of NUF1P1 — has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"To establish how P. falciparum NUF1P1 engages its partner ZNHIT3, this study asked what the physical basis of the interaction is and resolved the atomic structure of the complex.\",\n      \"evidence\": \"X-ray crystallography of the ZNHIT3–NUF1P1 complex with in vitro multimerization assays and AlphaFold comparison, in P. falciparum\",\n      \"pmids\": [\n        \"35315277\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No functional validation of NUF1P1 in the parasite; the biological consequence of the interaction is untested\",\n        \"The precise role of NUF1P1 in ribosome assembly or rRNA modification is not experimentally demonstrated here\",\n        \"Single lab, single study without independent confirmation\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether NUF1P1 functions in ribosome assembly, rRNA modification, or related pathways in the living parasite remains unestablished.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No in-parasite loss-of-function or localization data for NUF1P1\",\n        \"No identified substrate or downstream effector\",\n        \"No demonstration that the ZNHIT3 interaction is required for a specific cellular process\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0005515\",\n        \"supporting_discovery_ids\": [\n          0\n        ]\n      }\n    ],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [\n      \"ZNHIT3–NUF1P1 complex (PF3D7_1473900 with ZNHIT3)\"\n    ],\n    \"partners\": [\n      \"ZNHIT3\"\n    ],\n    \"other_free_text\": [\n      \"The ZNHIT3–NUF1P1 interaction is species-dependent and thermally stable, mediated by hydrophobic interface residues [#0].\",\n      \"The free ZNHIT3 fragment multimerizes in vitro and adopts conformations that bury the residues required for NUF1P1 binding [#0].\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_1473900","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_0916900). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1473900","name":null,"product":"ribosome assembly 1 protein","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1337000","name":null,"product":"conserved Plasmodium protein, unknown function","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1207200","name":null,"product":"ribosome assembly 1 protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"NUF1P1","evaluation":null}