{"gene":"PF3D7_0813300","run_date":"2026-09-08T12:51:27","timeline":{"discoveries":[{"year":2025,"finding":"PfNPM (PF3D7_0813300) N-terminal core domain adopts the characteristic pentameric doughnut conformation, and PfNPM exists as a pentamer in solution, as confirmed by crystal structure determination.","method":"X-ray crystallography and solution biochemistry","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure solved with solution validation (pentameric state confirmed biochemically), single lab but multiple orthogonal methods","pmids":["40049416"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"PfNPM (PF3D7_0813300) interacts individually with assembled H2A/H2B and H3/H4 histone dimers with equimolar stoichiometry; the acidic tracts of PfNPM are necessary for these interactions, and H3/H4 displays higher binding affinity than H2A/H2B, potentially due to stronger electrostatic interactions.","method":"Binding/interaction assays (affinity measurements) and acidic-tract mutagenesis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — direct binding assays with stoichiometry determination plus mutagenesis of acidic tracts, single lab with multiple orthogonal approaches","pmids":["40049416"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"H2A/H2B and H3/H4 likely share the same binding site on the PfNPM distal face, where H3/H4 can substitute H2A/H2B due to its higher binding affinity.","method":"Competition binding/interaction assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — inferred from binding affinity data in a single lab study; mechanistic conclusion supported by interaction data but not directly confirmed by structural mapping of the shared site","pmids":["40049416"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"PfNPM (PF3D7_0813300) does NOT interact directly with nucleosome core particles and does NOT display nucleosome assembly function, suggesting it is not directly involved in histone deposition onto parasite genomic DNA.","method":"In vitro nucleosome binding and nucleosome assembly assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — direct in vitro functional assays, but negative result from a single lab; reported explicitly as a negative/absence finding","pmids":["40049416"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"PfNPM (PF3D7_0813300) predominantly localizes to the nucleus and is expressed only in early blood stages (ring and trophozoite).","method":"Immunofluorescence assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single localization method (immunofluorescence), single lab, no direct functional consequence linked to localization","pmids":["40049416"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PfNPM (PF3D7_0813300) is a nuclear histone chaperone that forms a stable pentamer via its N-terminal core domain (confirmed by crystal structure), binds H2A/H2B and H3/H4 histone dimers through its acidic tracts with H3/H4 having higher affinity and potentially competing for the same distal-face binding site, yet does not directly interact with nucleosome core particles or perform nucleosome assembly, suggesting a non-canonical chaperoning role restricted to early blood-stage parasites."},"narrative":{"mechanistic_narrative":"PfNPM (PF3D7_0813300) is a nucleoplasmin-like histone-binding protein of Plasmodium falciparum that acts as a non-canonical histone chaperone in early blood-stage parasites [PMID:40049416]. Its N-terminal core domain adopts the characteristic pentameric doughnut fold and assembles into a stable pentamer in solution [PMID:40049416]. Through its acidic tracts, PfNPM binds assembled H2A/H2B and H3/H4 histone dimers with equimolar stoichiometry, with H3/H4 showing higher affinity — attributed to stronger electrostatic interactions — and apparently competing with H2A/H2B for a shared site on the distal face [PMID:40049416]. Despite this histone-binding activity, PfNPM does not interact with nucleosome core particles and shows no nucleosome assembly activity in vitro, indicating that it is not directly engaged in histone deposition onto genomic DNA [PMID:40049416]. Consistent with a chromatin-associated role restricted to a defined developmental window, PfNPM localizes predominantly to the nucleus and is expressed only in the ring and trophozoite stages [PMID:40049416]. Beyond these findings, no further mechanistic detail — including its in vivo function, regulatory partners, or the basis of its non-canonical behavior — has been characterized in the available corpus.","teleology":[{"year":2025,"claim":"Establishing the quaternary architecture of PfNPM was needed to place it within the nucleoplasmin/histone-chaperone family; the crystal structure resolved this by showing its core domain forms the signature pentamer.","evidence":"X-ray crystallography of the N-terminal core domain with solution biochemistry confirming the pentameric state","pmids":["40049416"],"confidence":"High","gaps":["Structure limited to the N-terminal core domain; the acidic tracts and full-length assembly are not structurally resolved","No structure of PfNPM bound to histones"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Whether PfNPM engages histones and by what determinants was unknown; binding assays plus acidic-tract mutagenesis showed it binds H2A/H2B and H3/H4 dimers via its acidic tracts, defining it as a histone-binding protein.","evidence":"Affinity binding assays with equimolar stoichiometry determination and acidic-tract mutagenesis","pmids":["40049416"],"confidence":"High","gaps":["The structural basis of dimer recognition is not mapped","In vivo relevance of these interactions untested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"To understand how PfNPM discriminates between histone types, competition assays indicated H2A/H2B and H3/H4 likely share the distal-face site, with the higher-affinity H3/H4 able to displace H2A/H2B.","evidence":"Competition binding/interaction assays inferring a shared site from relative affinities","pmids":["40049416"],"confidence":"Medium","gaps":["The shared binding site is inferred from affinity data, not confirmed by structural mapping","Single-lab study without independent replication"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Whether PfNPM performs canonical nucleosome assembly was tested directly; it neither binds nucleosome core particles nor assembles nucleosomes in vitro, distinguishing it from classical histone-deposition chaperones.","evidence":"In vitro nucleosome binding and nucleosome assembly assays (negative result)","pmids":["40049416"],"confidence":"Medium","gaps":["Negative in vitro result from a single lab; assay conditions may not capture all functions","The actual cellular role of PfNPM histone binding remains undefined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"To connect biochemistry to biology, localization and expression profiling placed PfNPM in the nucleus specifically during ring and trophozoite stages, bounding its function to early blood-stage chromatin biology.","evidence":"Immunofluorescence assay for subcellular localization and stage-specific expression","pmids":["40049416"],"confidence":"Medium","gaps":["Single localization method without functional consequence linked to localization","No genetic loss-of-function to establish stage-specific requirement"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The physiological function of PfNPM's non-canonical histone binding — including its in vivo essentiality, regulatory partners, and how histone chaperoning without nucleosome assembly contributes to early blood-stage parasite biology — remains unresolved.","evidence":"No experimental evidence in the available corpus addresses these questions","pmids":[],"confidence":"Medium","gaps":["No gene knockout/knockdown phenotype reported","No identified in vivo interacting partners or complex","Cellular role of histone binding absent nucleosome assembly undefined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Homopentamer formed via the N-terminal core domain [#0]"],"partners":["H2A/H2B HISTONE DIMER [#1]","H3/H4 HISTONE DIMER (HIGHER AFFINITY) [#1, #2]"],"other_free_text":["Binds histone dimers via acidic tracts but does not bind nucleosome core particles or assemble nucleosomes in vitro [#3]","Expressed only in ring and trophozoite (early blood) stages [#4]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"40049416","id":"PMC_40049416","title":"Structure-function studies of a nucleoplasmin isoform from Plasmodium falciparum.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40049416","citation_count":0,"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":3399,"output_tokens":1208,"usd":0.014158,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6040,"output_tokens":2351,"usd":0.044487,"stage2_stop_reason":"end_turn"},"total_usd":0.058645,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2025,\n      \"finding\": \"PfNPM (PF3D7_0813300) N-terminal core domain adopts the characteristic pentameric doughnut conformation, and PfNPM exists as a pentamer in solution, as confirmed by crystal structure determination.\",\n      \"method\": \"X-ray crystallography and solution biochemistry\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure solved with solution validation (pentameric state confirmed biochemically), single lab but multiple orthogonal methods\",\n      \"pmids\": [\"40049416\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PfNPM (PF3D7_0813300) interacts individually with assembled H2A/H2B and H3/H4 histone dimers with equimolar stoichiometry; the acidic tracts of PfNPM are necessary for these interactions, and H3/H4 displays higher binding affinity than H2A/H2B, potentially due to stronger electrostatic interactions.\",\n      \"method\": \"Binding/interaction assays (affinity measurements) and acidic-tract mutagenesis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — direct binding assays with stoichiometry determination plus mutagenesis of acidic tracts, single lab with multiple orthogonal approaches\",\n      \"pmids\": [\"40049416\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"H2A/H2B and H3/H4 likely share the same binding site on the PfNPM distal face, where H3/H4 can substitute H2A/H2B due to its higher binding affinity.\",\n      \"method\": \"Competition binding/interaction assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — inferred from binding affinity data in a single lab study; mechanistic conclusion supported by interaction data but not directly confirmed by structural mapping of the shared site\",\n      \"pmids\": [\"40049416\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PfNPM (PF3D7_0813300) does NOT interact directly with nucleosome core particles and does NOT display nucleosome assembly function, suggesting it is not directly involved in histone deposition onto parasite genomic DNA.\",\n      \"method\": \"In vitro nucleosome binding and nucleosome assembly assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — direct in vitro functional assays, but negative result from a single lab; reported explicitly as a negative/absence finding\",\n      \"pmids\": [\"40049416\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PfNPM (PF3D7_0813300) predominantly localizes to the nucleus and is expressed only in early blood stages (ring and trophozoite).\",\n      \"method\": \"Immunofluorescence assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single localization method (immunofluorescence), single lab, no direct functional consequence linked to localization\",\n      \"pmids\": [\"40049416\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PfNPM (PF3D7_0813300) is a nuclear histone chaperone that forms a stable pentamer via its N-terminal core domain (confirmed by crystal structure), binds H2A/H2B and H3/H4 histone dimers through its acidic tracts with H3/H4 having higher affinity and potentially competing for the same distal-face binding site, yet does not directly interact with nucleosome core particles or perform nucleosome assembly, suggesting a non-canonical chaperoning role restricted to early blood-stage parasites.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PfNPM (PF3D7_0813300) is a nucleoplasmin-like histone-binding protein of Plasmodium falciparum that acts as a non-canonical histone chaperone in early blood-stage parasites [#0, #1]. Its N-terminal core domain adopts the characteristic pentameric doughnut fold and assembles into a stable pentamer in solution [#0]. Through its acidic tracts, PfNPM binds assembled H2A/H2B and H3/H4 histone dimers with equimolar stoichiometry, with H3/H4 showing higher affinity — attributed to stronger electrostatic interactions — and apparently competing with H2A/H2B for a shared site on the distal face [#1, #2]. Despite this histone-binding activity, PfNPM does not interact with nucleosome core particles and shows no nucleosome assembly activity in vitro, indicating that it is not directly engaged in histone deposition onto genomic DNA [#3]. Consistent with a chromatin-associated role restricted to a defined developmental window, PfNPM localizes predominantly to the nucleus and is expressed only in the ring and trophozoite stages [#4]. Beyond these findings, no further mechanistic detail — including its in vivo function, regulatory partners, or the basis of its non-canonical behavior — has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2025,\n      \"claim\": \"Establishing the quaternary architecture of PfNPM was needed to place it within the nucleoplasmin/histone-chaperone family; the crystal structure resolved this by showing its core domain forms the signature pentamer.\",\n      \"evidence\": \"X-ray crystallography of the N-terminal core domain with solution biochemistry confirming the pentameric state\",\n      \"pmids\": [\"40049416\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure limited to the N-terminal core domain; the acidic tracts and full-length assembly are not structurally resolved\", \"No structure of PfNPM bound to histones\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether PfNPM engages histones and by what determinants was unknown; binding assays plus acidic-tract mutagenesis showed it binds H2A/H2B and H3/H4 dimers via its acidic tracts, defining it as a histone-binding protein.\",\n      \"evidence\": \"Affinity binding assays with equimolar stoichiometry determination and acidic-tract mutagenesis\",\n      \"pmids\": [\"40049416\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The structural basis of dimer recognition is not mapped\", \"In vivo relevance of these interactions untested\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"To understand how PfNPM discriminates between histone types, competition assays indicated H2A/H2B and H3/H4 likely share the distal-face site, with the higher-affinity H3/H4 able to displace H2A/H2B.\",\n      \"evidence\": \"Competition binding/interaction assays inferring a shared site from relative affinities\",\n      \"pmids\": [\"40049416\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The shared binding site is inferred from affinity data, not confirmed by structural mapping\", \"Single-lab study without independent replication\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Whether PfNPM performs canonical nucleosome assembly was tested directly; it neither binds nucleosome core particles nor assembles nucleosomes in vitro, distinguishing it from classical histone-deposition chaperones.\",\n      \"evidence\": \"In vitro nucleosome binding and nucleosome assembly assays (negative result)\",\n      \"pmids\": [\"40049416\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Negative in vitro result from a single lab; assay conditions may not capture all functions\", \"The actual cellular role of PfNPM histone binding remains undefined\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"To connect biochemistry to biology, localization and expression profiling placed PfNPM in the nucleus specifically during ring and trophozoite stages, bounding its function to early blood-stage chromatin biology.\",\n      \"evidence\": \"Immunofluorescence assay for subcellular localization and stage-specific expression\",\n      \"pmids\": [\"40049416\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single localization method without functional consequence linked to localization\", \"No genetic loss-of-function to establish stage-specific requirement\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The physiological function of PfNPM's non-canonical histone binding — including its in vivo essentiality, regulatory partners, and how histone chaperoning without nucleosome assembly contributes to early blood-stage parasite biology — remains unresolved.\",\n      \"evidence\": \"No experimental evidence in the available corpus addresses these questions\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No gene knockout/knockdown phenotype reported\", \"No identified in vivo interacting partners or complex\", \"Cellular role of histone binding absent nucleosome assembly undefined\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0042393\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"GO:0140713\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006325\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"complexes\": [\n      \"Homopentamer formed via the N-terminal core domain [#0]\"\n    ],\n    \"partners\": [\n      \"H2A/H2B histone dimer [#1]\",\n      \"H3/H4 histone dimer (higher affinity) [#1, #2]\"\n    ],\n    \"other_free_text\": [\n      \"Binds histone dimers via acidic tracts but does not bind nucleosome core particles or assemble nucleosomes in vitro [#3]\",\n      \"Expressed only in ring and trophozoite (early blood) stages [#4]\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_0813300","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_0617800, PF3D7_1105100). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0813300","name":null,"product":"NPL domain-containing protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1424300","name":null,"product":"NPL domain-containing protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1427100","name":null,"product":"NPL domain-containing protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}