{"gene":"PF3D7_0820000","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2024,"finding":"PF3D7_0820000 (SRCAP) was identified as a subunit of the PfSWR1 complex in P. falciparum. Reciprocal affinity pulldowns using PfEAF2::GFP (GFP-trap) identified 12 subunits of the PfSWR1 complex, with PF3D7_0820000 listed among the homologs of the yeast/human SWR1/SRCAP complex subunits. Both H2A.Z and H2B.Z were associated with the PfSWR1 complex, indicating the complex is involved in deposition of these variant histones.","method":"Reciprocal affinity pulldown (GFP-trap) with mass spectrometry / SAINT analysis","journal":"mSphere","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — reciprocal Co-IP with MS in a single lab; PF3D7_0820000 membership in PfSWR1 established but no direct functional assay performed on SRCAP itself","pmids":["38564734"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"finding":"PF3D7_0820000 (SRCAP) was identified as a yeast-two-hybrid interaction partner of PfCDPK6, predicted computationally to be involved in base excision repair and chromosome remodeling in P. falciparum.","method":"Yeast two-hybrid (Y2H) interaction screen; computational subnetwork alignment","journal":"BMC bioinformatics","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational prediction plus Y2H interaction; no direct functional experiment performed on PF3D7_0820000 itself","pmids":["24267797"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0820000 (SRCAP) is mechanistically established only as a subunit of the PfSWR1 chromatin-remodeling complex in P. falciparum, which associates with histone variants H2A.Z and H2B.Z and is implicated in their deposition; no direct enzymatic or functional experiments have been performed on PF3D7_0820000 itself."},"narrative":{"mechanistic_narrative":"PF3D7_0820000 (SRCAP) is established in the available corpus only as a subunit of the PfSWR1 chromatin-remodeling complex in P. falciparum, which associates with the variant histones H2A.Z and H2B.Z and is implicated in their deposition [PMID:38564734]. Its membership was defined by reciprocal affinity pulldowns of the complex rather than by any experiment on PF3D7_0820000 itself, so no direct enzymatic, remodeling, or functional activity has been demonstrated for the protein [PMID:38564734]. Beyond this complex membership and a low-confidence yeast-two-hybrid interaction with PfCDPK6 [PMID:24267797], no mechanistic detail specific to PF3D7_0820000 has been characterized in the available corpus.","teleology":[{"year":2013,"claim":"The first question was whether PF3D7_0820000 participates in any protein interaction network; a Y2H screen placed it as an interaction partner of PfCDPK6 and computationally linked it to base excision repair and chromosome remodeling, providing an initial but indirect hint of chromatin-related function.","evidence":"Yeast two-hybrid interaction screen with computational subnetwork alignment in P. falciparum","pmids":["24267797"],"confidence":"Low","gaps":["Y2H interaction with PfCDPK6 not independently confirmed and no direct functional assay on PF3D7_0820000","chromatin-remodeling role only computationally predicted, not experimentally tested","no localization or expression data for the protein"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"claim":"The question of which complex PF3D7_0820000 belongs to was answered by defining it as a subunit of the PfSWR1 chromatin-remodeling complex, establishing that the complex it resides in associates with and deposits the variant histones H2A.Z and H2B.Z.","evidence":"Reciprocal affinity pulldown (PfEAF2::GFP GFP-trap) with mass spectrometry and SAINT analysis in P. falciparum","pmids":["38564734"],"confidence":"Medium","gaps":["membership established but no direct functional assay performed on PF3D7_0820000 itself","specific contribution of PF3D7_0820000 to H2A.Z/H2B.Z deposition not resolved","no enzymatic, structural, or localization data specific to the subunit"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"It remains unknown what direct molecular activity PF3D7_0820000 contributes to the PfSWR1 complex and whether it is individually required for H2A.Z/H2B.Z deposition or parasite viability.","evidence":"","pmids":[],"confidence":"Low","gaps":["no genetic knockout or knockdown of PF3D7_0820000 reported","no reconstitution or biochemical activity assay for the subunit","no structural model of PF3D7_0820000 within PfSWR1"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["PfSWR1 chromatin-remodeling complex [#0]"],"partners":["PFEAF2 (CO-SUBUNIT OF PFSWR1) [#0]","H2A.Z / H2B.Z (ASSOCIATED VARIANT HISTONES) [#0]","PFCDPK6 (Y2H INTERACTOR, LOW CONFIDENCE) [#1]"],"other_free_text":["Established only as a subunit of the PfSWR1 complex implicated in H2A.Z/H2B.Z deposition; no direct functional or enzymatic experiment has been performed on PF3D7_0820000 itself [#0].","The Y2H interaction with PfCDPK6 and predicted involvement in base excision repair / chromosome remodeling is a low-confidence computational plus Y2H result [#1]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"37155862","id":"PMC_37155862","title":"Differentiation of Plasmodium male gametocytes is initiated by the recruitment of a chromatin remodeler to a male-specific cis-element.","date":"2023","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/37155862","citation_count":11,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["Snf2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38564734","id":"","title":"MYST regulates DNA repair and forms a NuA4-like complex in the malaria parasite Plasmodium falciparum.","date":"2024","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/38564734","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SRCAP"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"32552779","id":"","title":"Actin-related protein Arp4 regulates euchromatic gene expression and development through H2A.Z deposition in blood-stage Plasmodium falciparum.","date":"2020","source":"Parasites & vectors","url":"https://pubmed.ncbi.nlm.nih.gov/32552779","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SRCAP"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34855919","id":"","title":"\"Reading\" a new chapter in protozoan parasite transcriptional regulation.","date":"2021","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/34855919","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SRCAP"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24267797","id":"","title":"A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum.","date":"2013","source":"BMC bioinformatics","url":"https://pubmed.ncbi.nlm.nih.gov/24267797","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SRCAP"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23060959","id":"","title":"Plasmodium falciparum RuvB proteins: Emerging importance and expectations beyond cell cycle progression.","date":"2012","source":"Communicative & integrative biology","url":"https://pubmed.ncbi.nlm.nih.gov/23060959","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["SRCAP"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8958,"output_tokens":690,"usd":0.018612,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5264,"output_tokens":1563,"usd":0.032697,"stage2_stop_reason":"end_turn"},"total_usd":0.051309,"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\": 2024,\n      \"finding\": \"PF3D7_0820000 (SRCAP) was identified as a subunit of the PfSWR1 complex in P. falciparum. Reciprocal affinity pulldowns using PfEAF2::GFP (GFP-trap) identified 12 subunits of the PfSWR1 complex, with PF3D7_0820000 listed among the homologs of the yeast/human SWR1/SRCAP complex subunits. Both H2A.Z and H2B.Z were associated with the PfSWR1 complex, indicating the complex is involved in deposition of these variant histones.\",\n      \"method\": \"Reciprocal affinity pulldown (GFP-trap) with mass spectrometry / SAINT analysis\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — reciprocal Co-IP with MS in a single lab; PF3D7_0820000 membership in PfSWR1 established but no direct functional assay performed on SRCAP itself\",\n      \"pmids\": [\"38564734\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"PF3D7_0820000 (SRCAP) was identified as a yeast-two-hybrid interaction partner of PfCDPK6, predicted computationally to be involved in base excision repair and chromosome remodeling in P. falciparum.\",\n      \"method\": \"Yeast two-hybrid (Y2H) interaction screen; computational subnetwork alignment\",\n      \"journal\": \"BMC bioinformatics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational prediction plus Y2H interaction; no direct functional experiment performed on PF3D7_0820000 itself\",\n      \"pmids\": [\"24267797\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0820000 (SRCAP) is mechanistically established only as a subunit of the PfSWR1 chromatin-remodeling complex in P. falciparum, which associates with histone variants H2A.Z and H2B.Z and is implicated in their deposition; no direct enzymatic or functional experiments have been performed on PF3D7_0820000 itself.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0820000 (SRCAP) is established in the available corpus only as a subunit of the PfSWR1 chromatin-remodeling complex in P. falciparum, which associates with the variant histones H2A.Z and H2B.Z and is implicated in their deposition [#0]. Its membership was defined by reciprocal affinity pulldowns of the complex rather than by any experiment on PF3D7_0820000 itself, so no direct enzymatic, remodeling, or functional activity has been demonstrated for the protein [#0]. Beyond this complex membership and a low-confidence yeast-two-hybrid interaction with PfCDPK6 [#1], no mechanistic detail specific to PF3D7_0820000 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"The first question was whether PF3D7_0820000 participates in any protein interaction network; a Y2H screen placed it as an interaction partner of PfCDPK6 and computationally linked it to base excision repair and chromosome remodeling, providing an initial but indirect hint of chromatin-related function.\",\n      \"evidence\": \"Yeast two-hybrid interaction screen with computational subnetwork alignment in P. falciparum\",\n      \"pmids\": [\"24267797\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Y2H interaction with PfCDPK6 not independently confirmed and no direct functional assay on PF3D7_0820000\",\n        \"chromatin-remodeling role only computationally predicted, not experimentally tested\",\n        \"no localization or expression data for the protein\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"The question of which complex PF3D7_0820000 belongs to was answered by defining it as a subunit of the PfSWR1 chromatin-remodeling complex, establishing that the complex it resides in associates with and deposits the variant histones H2A.Z and H2B.Z.\",\n      \"evidence\": \"Reciprocal affinity pulldown (PfEAF2::GFP GFP-trap) with mass spectrometry and SAINT analysis in P. falciparum\",\n      \"pmids\": [\"38564734\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"membership established but no direct functional assay performed on PF3D7_0820000 itself\",\n        \"specific contribution of PF3D7_0820000 to H2A.Z/H2B.Z deposition not resolved\",\n        \"no enzymatic, structural, or localization data specific to the subunit\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown what direct molecular activity PF3D7_0820000 contributes to the PfSWR1 complex and whether it is individually required for H2A.Z/H2B.Z deposition or parasite viability.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"no genetic knockout or knockdown of PF3D7_0820000 reported\",\n        \"no reconstitution or biochemical activity assay for the subunit\",\n        \"no structural model of PF3D7_0820000 within PfSWR1\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006338\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"PfSWR1 chromatin-remodeling complex [#0]\"],\n    \"partners\": [\"PfEAF2 (co-subunit of PfSWR1) [#0]\", \"H2A.Z / H2B.Z (associated variant histones) [#0]\", \"PfCDPK6 (Y2H interactor, low confidence) [#1]\"],\n    \"other_free_text\": [\n      \"Established only as a subunit of the PfSWR1 complex implicated in H2A.Z/H2B.Z deposition; no direct functional or enzymatic experiment has been performed on PF3D7_0820000 itself [#0].\",\n      \"The Y2H interaction with PfCDPK6 and predicted involvement in base excision repair / chromosome remodeling is a low-confidence computational plus Y2H result [#1].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0820000","name":null,"product":"Snf2-related CBP activator, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0710800","name":null,"product":"Snf2-related CBP activator, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1313800","name":null,"product":"Snf2-related CBP activator, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"SRCAP","evaluation":null}