{"gene":"PF3D7_0905700","run_date":"2026-09-08T12:51:27","timeline":{"discoveries":[{"year":2012,"finding":"An Atg8 family interacting motif (AIM) was identified in P. falciparum ATG3 (residues 103–110) that directly binds PfAtg8. The co-crystal structure of PfAtg8 with the PfATG3(103–110) peptide was determined to 2.2 Å resolution, and in vitro interaction studies confirmed this binding. A unique Apicomplexan loop in PfAtg8 (absent from human Atg8 homologues) was shown to be important for PfATG3 binding. The protein-protein interaction between full-length PfAtg8 and PfATG3 was inhibited at low micromolar concentrations by 1,2,3-trihydroxybenzene.","method":"Co-crystal structure (X-ray crystallography, 2.2 Å), in vitro interaction assays, small-molecule inhibition of full-length protein-protein interaction","journal":"Journal of structural biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional validation by in vitro interaction studies and active-site-adjacent mutagenesis-equivalent structural analysis; multiple orthogonal methods in one study","pmids":["22982544"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"finding":"PbATG3 (the P. berghei ortholog of ATG3) is cotranscribed with PbATG7 and PbATG8 across all parasitic stages examined. Molecular analysis of the PbAtg8–PbAtg3 interaction revealed a novel mechanism compared with yeast and mammalian orthologs, further supported by the inability of Plasmodium ATG8 to functionally complement atg8Δ yeast or localize to autophagosomes in starved mammalian cells.","method":"Transcriptional co-expression analysis, molecular interaction analysis, cross-species functional complementation assay (yeast atg8Δ) and heterologous localization in mammalian cells","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — complementation and localization experiments in two heterologous systems, single lab, but multiple orthogonal approaches supporting a novel interaction mechanism","pmids":["24342964"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""},{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"finding":"Inhibitors identified by surface plasmon resonance against the PfAtg8–PfATG3 protein-protein interaction prevented PfAtg8 lipidation with phosphatidylethanolamine. This establishes PfATG3 as the E2-conjugating enzyme responsible for PfAtg8 lipidation, and shows that blocking the PfAtg8–PfATG3 interaction is sufficient to prevent this lipidation step and inhibit parasite growth in blood and liver stages.","method":"Surface plasmon resonance (protein-protein interaction inhibition), PfAtg8 lipidation assay (biochemical), P. falciparum blood-stage and liver-stage growth inhibition assays","journal":"Journal of medicinal chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — SPR plus biochemical lipidation assay plus cellular growth assay, single lab, two orthogonal methods confirming mechanistic role","pmids":["24786226"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"finding":"Virtual library screening targeting the unique A-loop of PfAtg8 (which mediates PfATG3 binding and is absent from human Atg8 homologues) identified small molecules that shift the lipidation state of PfAtg8 and inhibit P. falciparum growth in blood- and liver-stage cultures, confirming that the PfAtg8–PfATG3 interaction is essential for parasite survival.","method":"Virtual screening, surface plasmon resonance validation, PfAtg8 lipidation state assay, P. falciparum blood- and liver-stage growth inhibition","journal":"ChemMedChem","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in silico plus experimental SPR validation plus cellular lipidation assay, single lab, multiple orthogonal methods","pmids":["26748931"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"finding":"PfAtg8 is expressed during intra-erythrocytic development, associates with membranes as a likely lipid-conjugated form, and localizes to the apicoplast as shown by fluorescence microscopy and immunoelectron microscopy. No autophagosome-like structures were observed in erythrocytic stages, suggesting the ATG8 conjugation system (which includes ATG3) functions in apicoplast biology rather than canonical autophagy.","method":"Fluorescence microscopy, immunoelectron microscopy, biochemical membrane association assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two orthogonal imaging methods (fluorescence + immunoEM) for PfAtg8 localization; ATG3 implicated indirectly as part of the conjugation system; single lab","pmids":["22900071"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"P. falciparum ATG3 (PF3D7_0905700) functions as an E2-like conjugating enzyme that binds PfAtg8 via an Atg8-family interacting motif (AIM, residues 103–110) — structurally resolved to 2.2 Å — and catalyzes the lipidation of PfAtg8 with phosphatidylethanolamine; this interaction depends on a unique Apicomplexan loop in PfAtg8 absent from human homologues, and blocking the PfAtg8–PfATG3 protein-protein interaction prevents PfAtg8 lipidation and inhibits parasite growth, while the overall conjugation system appears dedicated to apicoplast maintenance rather than canonical autophagy in blood-stage parasites."},"narrative":{"mechanistic_narrative":"PF3D7_0905700 (ATG3) is the E2-like conjugating enzyme of the Plasmodium ATG8 conjugation system, catalyzing the lipidation of PfAtg8 with phosphatidylethanolamine [PMID:24786226]. ATG3 engages PfAtg8 through an Atg8-family interacting motif spanning residues 103–110, and the co-crystal structure of PfAtg8 bound to this ATG3 peptide, resolved to 2.2 Å, showed that binding depends on a unique Apicomplexan loop in PfAtg8 that is absent from human Atg8 homologues [PMID:22982544]. Disrupting the PfAtg8–ATG3 protein-protein interaction — whether by small molecules targeting the interface or the A-loop — prevents PfAtg8 lipidation and inhibits parasite growth in both blood and liver stages, establishing this interaction as essential for survival [PMID:24786226, PMID:26748931]. In P. berghei the ATG3 ortholog is cotranscribed with ATG7 and ATG8 across parasitic stages, and the PfAtg8–ATG3 interaction mechanism is divergent from yeast and mammalian systems [PMID:24342964]. The conjugation system in which ATG3 acts appears dedicated to apicoplast biology rather than canonical autophagy in blood-stage parasites, since lipidated PfAtg8 localizes to the apicoplast and no autophagosome-like structures form in erythrocytic stages [PMID:22900071].","teleology":[{"year":2012,"claim":"Establishing how ATG3 recognizes PfAtg8 was needed to define the molecular basis of the parasite conjugation machinery; the structure revealed a species-specific interaction interface.","evidence":"Co-crystal structure (2.2 Å) of PfAtg8 with the ATG3(103–110) AIM peptide plus in vitro interaction assays in P. falciparum","pmids":["22982544"],"confidence":"High","gaps":["Structure covers only the ATG3 AIM peptide, not full-length ATG3 or its catalytic architecture","Does not demonstrate the lipidation reaction itself"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2012,"claim":"The functional purpose of the ATG8 conjugation system in blood-stage parasites was unclear; localization of lipidated PfAtg8 to the apicoplast pointed toward a non-canonical, organelle-maintenance role rather than autophagy.","evidence":"Fluorescence and immunoelectron microscopy plus membrane-association biochemistry in P. falciparum; ATG3 implicated as a component of the conjugation system","pmids":["22900071"],"confidence":"Medium","gaps":["ATG3 itself was not directly localized, only inferred as part of the system","Does not exclude autophagy roles in other life-cycle stages"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"claim":"Whether the Plasmodium ATG3–ATG8 interaction mirrors yeast/mammalian machinery was open; cotranscription and failed heterologous complementation defined it as mechanistically divergent.","evidence":"Transcriptional co-expression analysis, cross-species complementation in atg8Δ yeast, and heterologous localization in starved mammalian cells for P. berghei (with P. falciparum)","pmids":["24342964"],"confidence":"Medium","gaps":["Interaction mechanism characterized indirectly through complementation failure","Does not resolve the catalytic mechanism of ATG3"],"attribution":[{"species":"Plasmodium berghei","strain":""},{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"claim":"It was unknown whether ATG3 is the enzyme driving PfAtg8 lipidation and whether blocking the interaction is sufficient to kill parasites; inhibitor studies assigned ATG3 the E2 role and validated it as a drug target.","evidence":"Surface plasmon resonance interaction inhibition, biochemical PfAtg8 lipidation assay, and blood- and liver-stage growth inhibition in P. falciparum","pmids":["24786226"],"confidence":"Medium","gaps":["E2 assignment inferred from interaction inhibition rather than direct enzymatic reconstitution of ATG3 catalysis","Single lab"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"claim":"To confirm the interaction is essential and druggable, the unique A-loop interface was targeted directly, yielding molecules that shift PfAtg8 lipidation and block growth.","evidence":"Virtual screening, SPR validation, PfAtg8 lipidation-state assay, and blood- and liver-stage growth inhibition in P. falciparum","pmids":["26748931"],"confidence":"Medium","gaps":["Effects on lipidation state read out on PfAtg8, not on ATG3 activity directly","Molecular consequences for apicoplast maintenance not resolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The catalytic mechanism of ATG3 as an E2 enzyme, its full-length structure, and its direct role in apicoplast biology remain to be defined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No direct enzymatic reconstitution of ATG3-catalyzed PfAtg8 lipidation","No full-length ATG3 structure","ATG3's own localization and phenotype under genetic ablation uncharacterized in the corpus"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Atg8 conjugation system"],"partners":["PFATG8","PBATG7 (COTRANSCRIBED, P. BERGHEI)","PBATG8 (COTRANSCRIBED, P. BERGHEI)"],"other_free_text":["Binds PfAtg8 via an Atg8-family interacting motif (AIM) at residues 103–110 [#0]","Interaction depends on a unique Apicomplexan A-loop in PfAtg8 absent from human homologues [#0, #3]","PfAtg8–ATG3 interaction inhibitable by small molecules (e.g. 1,2,3-trihydroxybenzene), preventing lipidation and inhibiting blood- and liver-stage growth [#0, #2, #3]","Conjugation system appears dedicated to apicoplast maintenance rather than canonical autophagy in blood stages [#4]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"22900071","id":"PMC_22900071","title":"Autophagy-related Atg8 localizes to the apicoplast of the human malaria parasite Plasmodium falciparum.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22900071","citation_count":69,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ATG3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23388496","id":"PMC_23388496","title":"Features of autophagic cell death in Plasmodium liver-stage parasites.","date":"2013","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/23388496","citation_count":56,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ATG3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22982544","id":"PMC_22982544","title":"Structural characterization and inhibition of the Plasmodium Atg8-Atg3 interaction.","date":"2012","source":"Journal of structural biology","url":"https://pubmed.ncbi.nlm.nih.gov/22982544","citation_count":45,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ATG3","PfATG3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24786226","id":"PMC_24786226","title":"Identification of an Atg8-Atg3 protein-protein interaction inhibitor from the medicines for Malaria Venture Malaria Box active in blood and liver stage Plasmodium falciparum parasites.","date":"2014","source":"Journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24786226","citation_count":40,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ATG3","PfATG3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24342964","id":"PMC_24342964","title":"Characterization of the ATG8-conjugation system in 2 Plasmodium species with special focus on the liver stage: possible linkage between the apicoplastic and autophagic systems?","date":"2013","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/24342964","citation_count":36,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PbATG3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23825614","id":"PMC_23825614","title":"Plasmodium falciparum erythrocytic stage parasites require the putative autophagy protein PfAtg7 for normal growth.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23825614","citation_count":26,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ATG3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26748931","id":"PMC_26748931","title":"Virtual Screening and Experimental Validation Identify Novel Inhibitors of the Plasmodium falciparum Atg8-Atg3 Protein-Protein Interaction.","date":"2016","source":"ChemMedChem","url":"https://pubmed.ncbi.nlm.nih.gov/26748931","citation_count":18,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ATG3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"29158278","id":"PMC_29158278","title":"Characterization of Plasmodium Atg3-Atg8 Interaction Inhibitors Identifies Novel Alternative Mechanisms of Action in Toxoplasma gondii.","date":"2018","source":"Antimicrobial agents and chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/29158278","citation_count":14,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ATG3","PfATG3"],"competing_organism_flag":true,"competing_organism_match":"Toxoplasma","competing_organism_only":true},{"pmid":"29383466","id":"PMC_29383466","title":"Structure-based drug design, synthesis and biological assays of P. falciparum Atg3-Atg8 protein-protein interaction inhibitors.","date":"2018","source":"Journal of computer-aided molecular design","url":"https://pubmed.ncbi.nlm.nih.gov/29383466","citation_count":11,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ATG3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"36869438","id":"PMC_36869438","title":"Biological functions and structural biology of Plasmodium falciparum autophagy-related proteins: The under-explored options for novel antimalarial drug design.","date":"2023","source":"Chemical biology & drug design","url":"https://pubmed.ncbi.nlm.nih.gov/36869438","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ATG3","PfATG3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"42473197","id":"PMC_42473197","title":"Divergent Autophagy Pathways in Plasmodium: Mechanisms, Functions, and Therapeutic Potential.","date":"2026","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/42473197","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ATG3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8045,"output_tokens":1769,"usd":0.025335,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6898,"output_tokens":2750,"usd":0.05162,"stage2_stop_reason":"end_turn"},"total_usd":0.076955,"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\": 2012,\n      \"finding\": \"An Atg8 family interacting motif (AIM) was identified in P. falciparum ATG3 (residues 103–110) that directly binds PfAtg8. The co-crystal structure of PfAtg8 with the PfATG3(103–110) peptide was determined to 2.2 Å resolution, and in vitro interaction studies confirmed this binding. A unique Apicomplexan loop in PfAtg8 (absent from human Atg8 homologues) was shown to be important for PfATG3 binding. The protein-protein interaction between full-length PfAtg8 and PfATG3 was inhibited at low micromolar concentrations by 1,2,3-trihydroxybenzene.\",\n      \"method\": \"Co-crystal structure (X-ray crystallography, 2.2 Å), in vitro interaction assays, small-molecule inhibition of full-length protein-protein interaction\",\n      \"journal\": \"Journal of structural biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional validation by in vitro interaction studies and active-site-adjacent mutagenesis-equivalent structural analysis; multiple orthogonal methods in one study\",\n      \"pmids\": [\"22982544\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"PbATG3 (the P. berghei ortholog of ATG3) is cotranscribed with PbATG7 and PbATG8 across all parasitic stages examined. Molecular analysis of the PbAtg8–PbAtg3 interaction revealed a novel mechanism compared with yeast and mammalian orthologs, further supported by the inability of Plasmodium ATG8 to functionally complement atg8Δ yeast or localize to autophagosomes in starved mammalian cells.\",\n      \"method\": \"Transcriptional co-expression analysis, molecular interaction analysis, cross-species functional complementation assay (yeast atg8Δ) and heterologous localization in mammalian cells\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — complementation and localization experiments in two heterologous systems, single lab, but multiple orthogonal approaches supporting a novel interaction mechanism\",\n      \"pmids\": [\"24342964\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}, {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Inhibitors identified by surface plasmon resonance against the PfAtg8–PfATG3 protein-protein interaction prevented PfAtg8 lipidation with phosphatidylethanolamine. This establishes PfATG3 as the E2-conjugating enzyme responsible for PfAtg8 lipidation, and shows that blocking the PfAtg8–PfATG3 interaction is sufficient to prevent this lipidation step and inhibit parasite growth in blood and liver stages.\",\n      \"method\": \"Surface plasmon resonance (protein-protein interaction inhibition), PfAtg8 lipidation assay (biochemical), P. falciparum blood-stage and liver-stage growth inhibition assays\",\n      \"journal\": \"Journal of medicinal chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — SPR plus biochemical lipidation assay plus cellular growth assay, single lab, two orthogonal methods confirming mechanistic role\",\n      \"pmids\": [\"24786226\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Virtual library screening targeting the unique A-loop of PfAtg8 (which mediates PfATG3 binding and is absent from human Atg8 homologues) identified small molecules that shift the lipidation state of PfAtg8 and inhibit P. falciparum growth in blood- and liver-stage cultures, confirming that the PfAtg8–PfATG3 interaction is essential for parasite survival.\",\n      \"method\": \"Virtual screening, surface plasmon resonance validation, PfAtg8 lipidation state assay, P. falciparum blood- and liver-stage growth inhibition\",\n      \"journal\": \"ChemMedChem\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in silico plus experimental SPR validation plus cellular lipidation assay, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"26748931\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"PfAtg8 is expressed during intra-erythrocytic development, associates with membranes as a likely lipid-conjugated form, and localizes to the apicoplast as shown by fluorescence microscopy and immunoelectron microscopy. No autophagosome-like structures were observed in erythrocytic stages, suggesting the ATG8 conjugation system (which includes ATG3) functions in apicoplast biology rather than canonical autophagy.\",\n      \"method\": \"Fluorescence microscopy, immunoelectron microscopy, biochemical membrane association assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two orthogonal imaging methods (fluorescence + immunoEM) for PfAtg8 localization; ATG3 implicated indirectly as part of the conjugation system; single lab\",\n      \"pmids\": [\"22900071\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"P. falciparum ATG3 (PF3D7_0905700) functions as an E2-like conjugating enzyme that binds PfAtg8 via an Atg8-family interacting motif (AIM, residues 103–110) — structurally resolved to 2.2 Å — and catalyzes the lipidation of PfAtg8 with phosphatidylethanolamine; this interaction depends on a unique Apicomplexan loop in PfAtg8 absent from human homologues, and blocking the PfAtg8–PfATG3 protein-protein interaction prevents PfAtg8 lipidation and inhibits parasite growth, while the overall conjugation system appears dedicated to apicoplast maintenance rather than canonical autophagy in blood-stage parasites.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0905700 (ATG3) is the E2-like conjugating enzyme of the Plasmodium ATG8 conjugation system, catalyzing the lipidation of PfAtg8 with phosphatidylethanolamine [#2]. ATG3 engages PfAtg8 through an Atg8-family interacting motif spanning residues 103\\u2013110, and the co-crystal structure of PfAtg8 bound to this ATG3 peptide, resolved to 2.2 \\u00c5, showed that binding depends on a unique Apicomplexan loop in PfAtg8 that is absent from human Atg8 homologues [#0]. Disrupting the PfAtg8\\u2013ATG3 protein-protein interaction \\u2014 whether by small molecules targeting the interface or the A-loop \\u2014 prevents PfAtg8 lipidation and inhibits parasite growth in both blood and liver stages, establishing this interaction as essential for survival [#2, #3]. In P. berghei the ATG3 ortholog is cotranscribed with ATG7 and ATG8 across parasitic stages, and the PfAtg8\\u2013ATG3 interaction mechanism is divergent from yeast and mammalian systems [#1]. The conjugation system in which ATG3 acts appears dedicated to apicoplast biology rather than canonical autophagy in blood-stage parasites, since lipidated PfAtg8 localizes to the apicoplast and no autophagosome-like structures form in erythrocytic stages [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Establishing how ATG3 recognizes PfAtg8 was needed to define the molecular basis of the parasite conjugation machinery; the structure revealed a species-specific interaction interface.\",\n      \"evidence\": \"Co-crystal structure (2.2 \\u00c5) of PfAtg8 with the ATG3(103\\u2013110) AIM peptide plus in vitro interaction assays in P. falciparum\",\n      \"pmids\": [\"22982544\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure covers only the ATG3 AIM peptide, not full-length ATG3 or its catalytic architecture\", \"Does not demonstrate the lipidation reaction itself\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"The functional purpose of the ATG8 conjugation system in blood-stage parasites was unclear; localization of lipidated PfAtg8 to the apicoplast pointed toward a non-canonical, organelle-maintenance role rather than autophagy.\",\n      \"evidence\": \"Fluorescence and immunoelectron microscopy plus membrane-association biochemistry in P. falciparum; ATG3 implicated as a component of the conjugation system\",\n      \"pmids\": [\"22900071\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"ATG3 itself was not directly localized, only inferred as part of the system\", \"Does not exclude autophagy roles in other life-cycle stages\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Whether the Plasmodium ATG3\\u2013ATG8 interaction mirrors yeast/mammalian machinery was open; cotranscription and failed heterologous complementation defined it as mechanistically divergent.\",\n      \"evidence\": \"Transcriptional co-expression analysis, cross-species complementation in atg8\\u0394 yeast, and heterologous localization in starved mammalian cells for P. berghei (with P. falciparum)\",\n      \"pmids\": [\"24342964\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Interaction mechanism characterized indirectly through complementation failure\", \"Does not resolve the catalytic mechanism of ATG3\"],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}, {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"It was unknown whether ATG3 is the enzyme driving PfAtg8 lipidation and whether blocking the interaction is sufficient to kill parasites; inhibitor studies assigned ATG3 the E2 role and validated it as a drug target.\",\n      \"evidence\": \"Surface plasmon resonance interaction inhibition, biochemical PfAtg8 lipidation assay, and blood- and liver-stage growth inhibition in P. falciparum\",\n      \"pmids\": [\"24786226\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E2 assignment inferred from interaction inhibition rather than direct enzymatic reconstitution of ATG3 catalysis\", \"Single lab\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"To confirm the interaction is essential and druggable, the unique A-loop interface was targeted directly, yielding molecules that shift PfAtg8 lipidation and block growth.\",\n      \"evidence\": \"Virtual screening, SPR validation, PfAtg8 lipidation-state assay, and blood- and liver-stage growth inhibition in P. falciparum\",\n      \"pmids\": [\"26748931\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Effects on lipidation state read out on PfAtg8, not on ATG3 activity directly\", \"Molecular consequences for apicoplast maintenance not resolved\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The catalytic mechanism of ATG3 as an E2 enzyme, its full-length structure, and its direct role in apicoplast biology remain to be defined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct enzymatic reconstitution of ATG3-catalyzed PfAtg8 lipidation\", \"No full-length ATG3 structure\", \"ATG3's own localization and phenotype under genetic ablation uncharacterized in the corpus\"],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0019776\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0019778\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"GO:0019786\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0020011\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006914\", \"supporting_discovery_ids\": [1, 4]},\n      {\"term_id\": \"GO:0016236\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"complexes\": [\"Atg8 conjugation system\"],\n    \"partners\": [\"PfAtg8\", \"PbAtg7 (cotranscribed, P. berghei)\", \"PbAtg8 (cotranscribed, P. berghei)\"],\n    \"other_free_text\": [\n      \"Binds PfAtg8 via an Atg8-family interacting motif (AIM) at residues 103\\u2013110 [#0]\",\n      \"Interaction depends on a unique Apicomplexan A-loop in PfAtg8 absent from human homologues [#0, #3]\",\n      \"PfAtg8\\u2013ATG3 interaction inhibitable by small molecules (e.g. 1,2,3-trihydroxybenzene), preventing lipidation and inhibiting blood- and liver-stage growth [#0, #2, #3]\",\n      \"Conjugation system appears dedicated to apicoplast maintenance rather than canonical autophagy in blood stages [#4]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0905700","name":null,"product":"autophagy-related protein 3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0415700","name":null,"product":"autophagy-related protein 3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0703400","name":null,"product":"autophagy-related protein 3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"ATG3","evaluation":null}