{"gene":"PF3D7_1219100","run_date":"2026-09-08T14:19:06","timeline":{"discoveries":[{"year":2020,"finding":"In reverse immunoprecipitation experiments using a clathrin nanobody, other heterotetrameric AP-complexes were shown to interact with clathrin (CHC/PF3D7_1219100), but AP-2 complex subunits were absent, demonstrating that CHC does not interact with the AP-2 complex in P. falciparum.","method":"Reverse immunoprecipitation with clathrin nanobody followed by mass spectrometry","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with nanobody plus MS identification, single lab, two orthogonal methods confirming absence of AP-2 interaction","pmids":["32098816"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2026,"finding":"CHC (PF3D7_1219100) localizes predominantly at the parasite periphery and near the cis-Golgi in P. falciparum trophozoites, and ultrastructural APEX2-based electron microscopy confirmed its presence at coated vesicle-like structures at the parasite periphery and at the collars of cytostomes.","method":"Live-cell imaging, immunofluorescence colocalization, and APEX2-based electron microscopy","journal":"Traffic (Copenhagen, Denmark)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization established by multiple orthogonal imaging methods (live-cell, IFA, EM), single lab","pmids":["41451970"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2026,"finding":"Interactome analyses confirmed that CHC (PF3D7_1219100) associates predominantly with AP-1 components and proteins involved in cytostome formation in P. falciparum, rather than with AP-2.","method":"Extensive interactome/co-immunoprecipitation mass spectrometry analyses","journal":"Traffic (Copenhagen, Denmark)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS-based interactome with multiple AP-1 components identified, single lab","pmids":["41451970"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2026,"finding":"Knockdown of CHC (PF3D7_1219100) in P. falciparum led to the formation of abnormally long cytostome tubes and impaired hemoglobin uptake, establishing that CHC is functionally required for cytostome-mediated endocytosis of host cytosol.","method":"Conditional knockdown with phenotypic readout (cytostome morphology and hemoglobin uptake assay)","journal":"Traffic (Copenhagen, Denmark)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined cellular phenotype (cytostome elongation + hemoglobin uptake defect), single lab","pmids":["41451970"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"Proximity labelling identified CHC (PF3D7_1219100) as a potential interactor of the PIP-binding protein PfPX2 (Pf3D7_0704400), which localizes to the Golgi and micronemes in P. falciparum schizonts, placing CHC in a potential vesicular trafficking pathway between the Golgi and micronemes.","method":"Proximity labelling (BioID-type) mass spectrometry","journal":"Scientific reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single proximity-labelling experiment identifying CHC as candidate interactor, no direct validation of CHC–PfPX2 interaction","pmids":["41125830"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"In P. falciparum, CHC (PF3D7_1219100) localizes at the parasite periphery and near the cis-Golgi at coated vesicle-like structures and at cytostome collars; it associates primarily with AP-1 (not AP-2) and is functionally required for cytostome-mediated endocytosis of host hemoglobin, as its knockdown produces abnormally elongated cytostome tubes and impaired hemoglobin uptake."},"narrative":{"mechanistic_narrative":"CHC (PF3D7_1219100) is the clathrin heavy chain of Plasmodium falciparum and functions in coated-vesicle traffic at the parasite periphery, where it is required for cytostome-mediated endocytosis of host cytosol [PMID:41451970]. It localizes predominantly at the parasite periphery and near the cis-Golgi, and ultrastructural APEX2-based electron microscopy places it at coated vesicle-like structures and at the collars of cytostomes [PMID:41451970]. Distinct from the canonical clathrin function in receptor-mediated endocytosis in other eukaryotes, CHC associates predominantly with AP-1 and cytostome-formation proteins and does not interact with the AP-2 complex, as reciprocal clathrin-nanobody immunoprecipitation and interactome mass spectrometry both failed to recover AP-2 subunits [PMID:32098816, PMID:41451970]. Conditional knockdown produces abnormally elongated cytostome tubes and impaired hemoglobin uptake, establishing CHC as functionally required for cytostome-mediated host-cytosol endocytosis [PMID:41451970]. Beyond these findings, no further mechanistic detail—including structural characterization or the biochemical basis of its AP-1 selectivity—has been characterized in the available corpus.","teleology":[{"year":2020,"claim":"Whether P. falciparum clathrin uses the canonical AP-2 adaptor for endocytosis was unknown; reciprocal immunoprecipitation resolved which adaptor complexes CHC engages.","evidence":"Reverse immunoprecipitation with a clathrin nanobody followed by mass spectrometry","pmids":["32098816"],"confidence":"Medium","gaps":["Does not identify which specific AP-1 subunits mediate the interaction","Does not establish the functional consequence of AP-2 absence","Absence of AP-2 in the pulldown does not exclude transient or context-specific contacts"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Proximity labelling asked whether CHC participates in Golgi-to-microneme traffic by placing it near a PIP-binding protein.","evidence":"BioID-type proximity labelling mass spectrometry of PfPX2 (Pf3D7_0704400)","pmids":["41125830"],"confidence":"Low","gaps":["Single proximity-labelling experiment with no direct validation of the CHC–PfPX2 interaction","Does not establish that CHC functions in the Golgi-to-microneme pathway","Proximity does not distinguish direct binding from shared compartment residence"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2026,"claim":"The subcellular site of CHC action was unresolved; multi-modal imaging localized it to coated vesicles and cytostome collars, defining where it operates.","evidence":"Live-cell imaging, immunofluorescence colocalization, and APEX2-based electron microscopy in trophozoites","pmids":["41451970"],"confidence":"Medium","gaps":["Does not resolve whether the peripheral and cis-Golgi pools represent distinct functional roles","Ultrastructural assignment does not establish the composition of the coats it forms"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2026,"claim":"Whether CHC is functionally required for host-cytosol uptake was unknown; conditional knockdown established a causal role in cytostome-mediated endocytosis.","evidence":"Conditional knockdown with cytostome-morphology and hemoglobin-uptake readouts, plus interactome mass spectrometry confirming AP-1 (not AP-2) association","pmids":["41451970"],"confidence":"Medium","gaps":["Mechanism by which loss of CHC produces elongated cytostome tubes is not defined","Does not identify the molecular step (invagination, scission, coat assembly) that fails on knockdown","Single-lab loss-of-function without orthogonal genetic complementation"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"How CHC selectively partners with AP-1 rather than AP-2 and how it drives cytostome scission remain undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the CHC coat or its adaptor interface","The biochemical basis of AP-1 selectivity is uncharacterized","The CHC–PfPX2 link and any Golgi-to-microneme role remain unvalidated"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Associates with the AP-1 adaptor complex; does not interact with the AP-2 complex"],"partners":["AP-1 ADAPTOR COMPLEX SUBUNITS (INTERACTOME/CO-IP)","CYTOSTOME-FORMATION PROTEINS","PFPX2 (PF3D7_0704400) — CANDIDATE PROXIMITY INTERACTOR, UNVALIDATED"],"other_free_text":["Knockdown produces abnormally elongated cytostome tubes and impaired hemoglobin uptake, indicating a functional role in cytostome-mediated host-cytosol endocytosis.","Localized to coated vesicle-like structures at the parasite periphery and at cytostome collars by APEX2 electron microscopy."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"32098816","id":"PMC_32098816","title":"The Plasmodium falciparum Artemisinin Susceptibility-Associated AP-2 Adaptin μ Subunit is Clathrin Independent and Essential for Schizont Maturation.","date":"2020","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/32098816","citation_count":33,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38759952","id":"PMC_38759952","title":"Proteomes of plasmodium knowlesi early and late ring-stage parasites and infected host erythrocytes.","date":"2024","source":"Journal of proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/38759952","citation_count":4,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["clathrin heavy chain"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41451970","id":"PMC_41451970","title":"Clathrins Are Involved in the Endocytosis of Host Cytosol in the Malaria Parasite.","date":"2026","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/41451970","citation_count":2,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["clathrin heavy chain"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41125830","id":"PMC_41125830","title":"Characterization of a phosphoinositide-binding protein containing a PHOX homology domain in the malaria parasite Plasmodium falciparum.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/41125830","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["clathrin heavy chain"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5760,"output_tokens":1315,"usd":0.018503,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6224,"output_tokens":2342,"usd":0.044835,"stage2_stop_reason":"end_turn"},"total_usd":0.063338,"stage1_batch_id":"msgbatch_011BPjN2BL33F8cJXD1r7V7T","stage2_batch_id":"msgbatch_01Qwg6vP7qxkpL6Gsc7tajsb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2020,\n      \"finding\": \"In reverse immunoprecipitation experiments using a clathrin nanobody, other heterotetrameric AP-complexes were shown to interact with clathrin (CHC/PF3D7_1219100), but AP-2 complex subunits were absent, demonstrating that CHC does not interact with the AP-2 complex in P. falciparum.\",\n      \"method\": \"Reverse immunoprecipitation with clathrin nanobody followed by mass spectrometry\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with nanobody plus MS identification, single lab, two orthogonal methods confirming absence of AP-2 interaction\",\n      \"pmids\": [\"32098816\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"CHC (PF3D7_1219100) localizes predominantly at the parasite periphery and near the cis-Golgi in P. falciparum trophozoites, and ultrastructural APEX2-based electron microscopy confirmed its presence at coated vesicle-like structures at the parasite periphery and at the collars of cytostomes.\",\n      \"method\": \"Live-cell imaging, immunofluorescence colocalization, and APEX2-based electron microscopy\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization established by multiple orthogonal imaging methods (live-cell, IFA, EM), single lab\",\n      \"pmids\": [\"41451970\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Interactome analyses confirmed that CHC (PF3D7_1219100) associates predominantly with AP-1 components and proteins involved in cytostome formation in P. falciparum, rather than with AP-2.\",\n      \"method\": \"Extensive interactome/co-immunoprecipitation mass spectrometry analyses\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS-based interactome with multiple AP-1 components identified, single lab\",\n      \"pmids\": [\"41451970\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Knockdown of CHC (PF3D7_1219100) in P. falciparum led to the formation of abnormally long cytostome tubes and impaired hemoglobin uptake, establishing that CHC is functionally required for cytostome-mediated endocytosis of host cytosol.\",\n      \"method\": \"Conditional knockdown with phenotypic readout (cytostome morphology and hemoglobin uptake assay)\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined cellular phenotype (cytostome elongation + hemoglobin uptake defect), single lab\",\n      \"pmids\": [\"41451970\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Proximity labelling identified CHC (PF3D7_1219100) as a potential interactor of the PIP-binding protein PfPX2 (Pf3D7_0704400), which localizes to the Golgi and micronemes in P. falciparum schizonts, placing CHC in a potential vesicular trafficking pathway between the Golgi and micronemes.\",\n      \"method\": \"Proximity labelling (BioID-type) mass spectrometry\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single proximity-labelling experiment identifying CHC as candidate interactor, no direct validation of CHC–PfPX2 interaction\",\n      \"pmids\": [\"41125830\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"In P. falciparum, CHC (PF3D7_1219100) localizes at the parasite periphery and near the cis-Golgi at coated vesicle-like structures and at cytostome collars; it associates primarily with AP-1 (not AP-2) and is functionally required for cytostome-mediated endocytosis of host hemoglobin, as its knockdown produces abnormally elongated cytostome tubes and impaired hemoglobin uptake.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CHC (PF3D7_1219100) is the clathrin heavy chain of Plasmodium falciparum and functions in coated-vesicle traffic at the parasite periphery, where it is required for cytostome-mediated endocytosis of host cytosol [#1, #3]. It localizes predominantly at the parasite periphery and near the cis-Golgi, and ultrastructural APEX2-based electron microscopy places it at coated vesicle-like structures and at the collars of cytostomes [#1]. Distinct from the canonical clathrin function in receptor-mediated endocytosis in other eukaryotes, CHC associates predominantly with AP-1 and cytostome-formation proteins and does not interact with the AP-2 complex, as reciprocal clathrin-nanobody immunoprecipitation and interactome mass spectrometry both failed to recover AP-2 subunits [#0, #2]. Conditional knockdown produces abnormally elongated cytostome tubes and impaired hemoglobin uptake, establishing CHC as functionally required for cytostome-mediated host-cytosol endocytosis [#3]. Beyond these findings, no further mechanistic detail\\u2014including structural characterization or the biochemical basis of its AP-1 selectivity\\u2014has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2020,\n      \"claim\": \"Whether P. falciparum clathrin uses the canonical AP-2 adaptor for endocytosis was unknown; reciprocal immunoprecipitation resolved which adaptor complexes CHC engages.\",\n      \"evidence\": \"Reverse immunoprecipitation with a clathrin nanobody followed by mass spectrometry\",\n      \"pmids\": [\"32098816\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Does not identify which specific AP-1 subunits mediate the interaction\",\n        \"Does not establish the functional consequence of AP-2 absence\",\n        \"Absence of AP-2 in the pulldown does not exclude transient or context-specific contacts\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Proximity labelling asked whether CHC participates in Golgi-to-microneme traffic by placing it near a PIP-binding protein.\",\n      \"evidence\": \"BioID-type proximity labelling mass spectrometry of PfPX2 (Pf3D7_0704400)\",\n      \"pmids\": [\"41125830\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single proximity-labelling experiment with no direct validation of the CHC\\u2013PfPX2 interaction\",\n        \"Does not establish that CHC functions in the Golgi-to-microneme pathway\",\n        \"Proximity does not distinguish direct binding from shared compartment residence\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"The subcellular site of CHC action was unresolved; multi-modal imaging localized it to coated vesicles and cytostome collars, defining where it operates.\",\n      \"evidence\": \"Live-cell imaging, immunofluorescence colocalization, and APEX2-based electron microscopy in trophozoites\",\n      \"pmids\": [\"41451970\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Does not resolve whether the peripheral and cis-Golgi pools represent distinct functional roles\",\n        \"Ultrastructural assignment does not establish the composition of the coats it forms\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Whether CHC is functionally required for host-cytosol uptake was unknown; conditional knockdown established a causal role in cytostome-mediated endocytosis.\",\n      \"evidence\": \"Conditional knockdown with cytostome-morphology and hemoglobin-uptake readouts, plus interactome mass spectrometry confirming AP-1 (not AP-2) association\",\n      \"pmids\": [\"41451970\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which loss of CHC produces elongated cytostome tubes is not defined\",\n        \"Does not identify the molecular step (invagination, scission, coat assembly) that fails on knockdown\",\n        \"Single-lab loss-of-function without orthogonal genetic complementation\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CHC selectively partners with AP-1 rather than AP-2 and how it drives cytostome scission remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural model of the CHC coat or its adaptor interface\",\n        \"The biochemical basis of AP-1 selectivity is uncharacterized\",\n        \"The CHC\\u2013PfPX2 link and any Golgi-to-microneme role remain unvalidated\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0032050\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0030136\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0071944\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006897\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0016192\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"complexes\": [\n      \"Associates with the AP-1 adaptor complex; does not interact with the AP-2 complex\"\n    ],\n    \"partners\": [\n      \"AP-1 adaptor complex subunits (interactome/Co-IP)\",\n      \"Cytostome-formation proteins\",\n      \"PfPX2 (Pf3D7_0704400) — candidate proximity interactor, unvalidated\"\n    ],\n    \"other_free_text\": [\n      \"Knockdown produces abnormally elongated cytostome tubes and impaired hemoglobin uptake, indicating a functional role in cytostome-mediated host-cytosol endocytosis.\",\n      \"Localized to coated vesicle-like structures at the parasite periphery and at cytostome collars by APEX2 electron microscopy.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1219100","name":null,"product":"clathrin heavy chain, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1434700","name":null,"product":"clathrin heavy chain, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1438700","name":null,"product":"clathrin heavy chain, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"CHC","evaluation":null}