{"gene":"PF3D7_0110500","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2019,"finding":"BDP3 (PF3D7_0110500) was identified as a putative epigenetic reader protein in P. falciparum through histone peptide pull-down proteomics, establishing its membership in the set of PTM-reader proteins associated with acetylated histone marks.","method":"Quantitative histone peptide pull-down followed by mass spectrometry (interaction proteomics)","journal":"Nucleic acids research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/pull-down approach, single lab, no functional follow-up specific to BDP3; BDP3 detected as a hit but not individually validated","pmids":["31728527"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"finding":"BDP3 (PF3D7_0110500) was identified as an interaction partner of PfMORC by immunoprecipitation followed by mass spectrometry, placing it within a nuclear chromatin-modulation network that includes HDAC1, SET3, PHD2, ISWI, and multiple ApiAP2 transcription factors.","method":"Immunoprecipitation (IP) followed by mass spectrometry (IP-MS) using PfMORC-HA tagged parasites","journal":"eLife","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/pull-down, single lab; BDP3 detected as an enriched interactor of PfMORC but no functional experiments performed specifically on BDP3","pmids":["39636094"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"finding":"BDP3 (PF3D7_0110500) was identified as an interactor of PfSET10 by TurboID proximity-labelling coupled with mass spectrometry, further supporting its membership in a broader nuclear chromatin modulation network in blood-stage parasites.","method":"TurboID proximity-labelling coupled with mass spectrometry","journal":"mSphere","confidence":"Low","confidence_rationale":"Tier 3 / Weak — proximity-labelling (not direct Co-IP), single lab, no functional experiments specific to BDP3","pmids":["39445823"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"BDP3 (PF3D7_0110500) is a putative bromodomain-containing epigenetic reader protein in P. falciparum that has been detected as an interaction partner of PfMORC and PfSET10 by proteomic approaches, placing it within a nuclear chromatin-modulation network; no direct enzymatic activity, substrate specificity, structure, or loss-of-function phenotype has been experimentally established for BDP3 itself."},"narrative":{"mechanistic_narrative":"BDP3 (PF3D7_0110500) is a putative bromodomain-containing epigenetic reader protein in Plasmodium falciparum, identified through histone peptide pull-down proteomics as a member of the set of PTM-reader proteins associated with acetylated histone marks [PMID:31728527]. Beyond this candidate reader assignment, BDP3 has been detected only as a component of a nuclear chromatin-modulation network: it co-purifies with PfMORC alongside HDAC1, SET3, PHD2, ISWI, and multiple ApiAP2 transcription factors [PMID:39636094], and appears in the proximity interactome of PfSET10 [PMID:39445823]. All three observations are proteomic detections; no direct enzymatic activity, substrate or histone-mark specificity, structure, subcellular localization, or loss-of-function phenotype has been experimentally established for BDP3 itself in the available corpus. The current evidence therefore places BDP3 within a blood-stage chromatin-modulation network by association only, and does not define its individual molecular role.","teleology":[{"year":2019,"claim":"To ask whether BDP3 acts as a chromatin reader, histone peptide affinity proteomics tested which parasite proteins bind modified histone tails, and placed BDP3 among candidate acetyl-histone readers.","evidence":"Quantitative histone peptide pull-down with mass spectrometry in P. falciparum","pmids":["31728527"],"confidence":"Low","gaps":["Single pull-down hit not individually validated; direct binding of BDP3 to a defined histone mark not confirmed","No specific acetyl-lysine mark or affinity measured for BDP3","No demonstration that the bromodomain of BDP3 mediates the interaction"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"claim":"To position BDP3 in a functional chromatin context, IP-MS of tagged PfMORC asked which proteins co-assemble with it, recovering BDP3 within a network including HDAC1, SET3, PHD2, ISWI, and ApiAP2 factors.","evidence":"Immunoprecipitation-mass spectrometry using PfMORC-HA tagged P. falciparum parasites","pmids":["39636094"],"confidence":"Low","gaps":["Single Co-IP without reciprocal pull-down from BDP3; direct vs indirect association undetermined","No functional experiment performed on BDP3 within the network","Stoichiometry and whether BDP3 is a stable versus transient component are unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"claim":"Proximity labelling of PfSET10 tested BDP3's spatial proximity to another chromatin regulator, independently supporting its membership in a blood-stage nuclear chromatin-modulation network.","evidence":"TurboID proximity-labelling coupled with mass spectrometry in blood-stage P. falciparum","pmids":["39445823"],"confidence":"Low","gaps":["Proximity labelling indicates neighborhood, not direct interaction","No validation of BDP3-PfSET10 association by orthogonal method","No functional consequence of the association tested for BDP3"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The direct molecular function of BDP3 remains undefined: whether its bromodomain binds a specific acetylated histone mark, its subcellular localization, and its loss-of-function phenotype are all unestablished.","evidence":"No direct functional, structural, or genetic characterization of BDP3 in the available corpus","pmids":[],"confidence":"Low","gaps":["No histone-mark binding specificity or affinity determined for BDP3","No knockout/knockdown phenotype or essentiality data for BDP3","No structural model or localization data specific to BDP3"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["PfMORC-associated nuclear chromatin-modulation network (with HDAC1, SET3, PHD2, ISWI, ApiAP2 transcription factors) [#1]"],"partners":["PFMORC [#1]","PFSET10 (PROXIMITY INTERACTOR) [#2]"],"other_free_text":["Identified as a candidate acetyl-histone reader by histone peptide pull-down; assigned as a putative bromodomain protein but bromodomain-mark binding not directly demonstrated [#0]","All evidence for BDP3 derives from proteomic detection (pull-down, IP-MS, proximity labelling); no functional experiment has been performed specifically on BDP3 [#0, #1, #2]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"31728527","id":"PMC_31728527","title":"Epigenetic reader complexes of the human malaria parasite, Plasmodium falciparum.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/31728527","citation_count":48,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39445823","id":"","title":"The Plasmodium falciparum histone methyltransferase SET10 participates in a chromatin modulation network crucial for intraerythrocytic development.","date":"2024","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/39445823","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["BDP3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39636094","id":"","title":"PfMORC protein regulates chromatin accessibility and transcriptional repression in the human malaria parasite, Plasmodium falciparum.","date":"2024","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/39636094","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["BDP3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"36328269","id":"","title":"Structural insights into acetylated histone ligand recognition by the BDP1 bromodomain of Plasmodium falciparum.","date":"2022","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/36328269","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["BDP3"],"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":["BDP3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35493110","id":"","title":"The Putative Bromodomain Protein PfBDP7 of the Human Malaria Parasite Plasmodium Falciparum Cooperates With PfBDP1 in the Silencing of Variant Surface Antigen Expression.","date":"2022","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/35493110","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["BDP3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9413,"output_tokens":844,"usd":0.020449,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5533,"output_tokens":1963,"usd":0.03837,"stage2_stop_reason":"end_turn"},"total_usd":0.058819,"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\": 2019,\n      \"finding\": \"BDP3 (PF3D7_0110500) was identified as a putative epigenetic reader protein in P. falciparum through histone peptide pull-down proteomics, establishing its membership in the set of PTM-reader proteins associated with acetylated histone marks.\",\n      \"method\": \"Quantitative histone peptide pull-down followed by mass spectrometry (interaction proteomics)\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/pull-down approach, single lab, no functional follow-up specific to BDP3; BDP3 detected as a hit but not individually validated\",\n      \"pmids\": [\"31728527\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"BDP3 (PF3D7_0110500) was identified as an interaction partner of PfMORC by immunoprecipitation followed by mass spectrometry, placing it within a nuclear chromatin-modulation network that includes HDAC1, SET3, PHD2, ISWI, and multiple ApiAP2 transcription factors.\",\n      \"method\": \"Immunoprecipitation (IP) followed by mass spectrometry (IP-MS) using PfMORC-HA tagged parasites\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/pull-down, single lab; BDP3 detected as an enriched interactor of PfMORC but no functional experiments performed specifically on BDP3\",\n      \"pmids\": [\"39636094\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"BDP3 (PF3D7_0110500) was identified as an interactor of PfSET10 by TurboID proximity-labelling coupled with mass spectrometry, further supporting its membership in a broader nuclear chromatin modulation network in blood-stage parasites.\",\n      \"method\": \"TurboID proximity-labelling coupled with mass spectrometry\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — proximity-labelling (not direct Co-IP), single lab, no functional experiments specific to BDP3\",\n      \"pmids\": [\"39445823\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"BDP3 (PF3D7_0110500) is a putative bromodomain-containing epigenetic reader protein in P. falciparum that has been detected as an interaction partner of PfMORC and PfSET10 by proteomic approaches, placing it within a nuclear chromatin-modulation network; no direct enzymatic activity, substrate specificity, structure, or loss-of-function phenotype has been experimentally established for BDP3 itself.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"BDP3 (PF3D7_0110500) is a putative bromodomain-containing epigenetic reader protein in Plasmodium falciparum, identified through histone peptide pull-down proteomics as a member of the set of PTM-reader proteins associated with acetylated histone marks [#0]. Beyond this candidate reader assignment, BDP3 has been detected only as a component of a nuclear chromatin-modulation network: it co-purifies with PfMORC alongside HDAC1, SET3, PHD2, ISWI, and multiple ApiAP2 transcription factors [#1], and appears in the proximity interactome of PfSET10 [#2]. All three observations are proteomic detections; no direct enzymatic activity, substrate or histone-mark specificity, structure, subcellular localization, or loss-of-function phenotype has been experimentally established for BDP3 itself in the available corpus. The current evidence therefore places BDP3 within a blood-stage chromatin-modulation network by association only, and does not define its individual molecular role.\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"To ask whether BDP3 acts as a chromatin reader, histone peptide affinity proteomics tested which parasite proteins bind modified histone tails, and placed BDP3 among candidate acetyl-histone readers.\",\n      \"evidence\": \"Quantitative histone peptide pull-down with mass spectrometry in P. falciparum\",\n      \"pmids\": [\"31728527\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single pull-down hit not individually validated; direct binding of BDP3 to a defined histone mark not confirmed\",\n        \"No specific acetyl-lysine mark or affinity measured for BDP3\",\n        \"No demonstration that the bromodomain of BDP3 mediates the interaction\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"To position BDP3 in a functional chromatin context, IP-MS of tagged PfMORC asked which proteins co-assemble with it, recovering BDP3 within a network including HDAC1, SET3, PHD2, ISWI, and ApiAP2 factors.\",\n      \"evidence\": \"Immunoprecipitation-mass spectrometry using PfMORC-HA tagged P. falciparum parasites\",\n      \"pmids\": [\"39636094\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single Co-IP without reciprocal pull-down from BDP3; direct vs indirect association undetermined\",\n        \"No functional experiment performed on BDP3 within the network\",\n        \"Stoichiometry and whether BDP3 is a stable versus transient component are unknown\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Proximity labelling of PfSET10 tested BDP3's spatial proximity to another chromatin regulator, independently supporting its membership in a blood-stage nuclear chromatin-modulation network.\",\n      \"evidence\": \"TurboID proximity-labelling coupled with mass spectrometry in blood-stage P. falciparum\",\n      \"pmids\": [\"39445823\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Proximity labelling indicates neighborhood, not direct interaction\",\n        \"No validation of BDP3-PfSET10 association by orthogonal method\",\n        \"No functional consequence of the association tested for BDP3\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct molecular function of BDP3 remains undefined: whether its bromodomain binds a specific acetylated histone mark, its subcellular localization, and its loss-of-function phenotype are all unestablished.\",\n      \"evidence\": \"No direct functional, structural, or genetic characterization of BDP3 in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No histone-mark binding specificity or affinity determined for BDP3\",\n        \"No knockout/knockdown phenotype or essentiality data for BDP3\",\n        \"No structural model or localization data specific to BDP3\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140566\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006325\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"complexes\": [\n      \"PfMORC-associated nuclear chromatin-modulation network (with HDAC1, SET3, PHD2, ISWI, ApiAP2 transcription factors) [#1]\"\n    ],\n    \"partners\": [\n      \"PfMORC [#1]\",\n      \"PfSET10 (proximity interactor) [#2]\"\n    ],\n    \"other_free_text\": [\n      \"Identified as a candidate acetyl-histone reader by histone peptide pull-down; assigned as a putative bromodomain protein but bromodomain-mark binding not directly demonstrated [#0]\",\n      \"All evidence for BDP3 derives from proteomic detection (pull-down, IP-MS, proximity labelling); no functional experiment has been performed specifically on BDP3 [#0, #1, #2]\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_0110500","tier":"GROUNDING","verdict":"Evidence-grounding concern","subtype":"uncited_synthesis","uniprot_band":"empty","rules_fired":"R8","issue":"R8: 1/3 claims uncited (33%)"},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0110500","name":null,"product":"bromodomain protein 3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0203200","name":null,"product":"bromodomain protein 3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0203400","name":null,"product":"bromodomain protein 3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"BDP3","evaluation":null}