{"gene":"ATP5PB","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":2017,"finding":"Genetic disruption of ATP5F1 (subunit b membrane domain) in HAP1 cells (HAP1-Δb) demonstrated that the membrane domain of subunit b does not contribute to formation of the mitochondrial permeability transition pore (PTP), as the characteristic PTP properties were preserved in cells lacking this domain.","method":"CRISPR/gene disruption generating clonal HAP1-Δb cells, functional PTP assay (calcium-triggered swelling, cyclosporin A sensitivity)","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic knockout with defined functional readout, complemented by parallel OSCP knockout, rigorous controls, published in peer-reviewed journal","pmids":["28784775"],"is_preprint":false},{"year":2013,"finding":"ATP5F1 (subunit b of the ATP synthase F0 complex) directly interacts with cardiolipin in cardiac interfibrillar mitochondria; this interaction is significantly decreased in type 1 diabetic interfibrillar mitochondria, coinciding with reduced ATP synthase activity.","method":"Co-immunoprecipitation/direct interaction assay between cardiolipin and ATP synthase subunits in isolated cardiac mitochondrial subpopulations; Western blot for protein content; enzymatic activity assay for ATP synthase","journal":"Life sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct interaction identified by pulldown/co-IP in isolated mitochondria with functional enzymatic activity readout, single lab","pmids":["23872101"],"is_preprint":false},{"year":2026,"finding":"6PPDQ covalently binds to ATP5PB (subunit b of ATP synthase) via its cysteine residues, and this binding is associated with decreased Complex I and IV enzymatic activities, reduced cellular ATP content, reduced mitochondrial membrane potential, and elevated mitochondrial ROS.","method":"Sulfhydryl-reactive proteomics platform identifying covalent binding targets; enzymatic activity assays for mitochondrial respiratory chain complexes I and IV; ATP content measurement; mitochondrial membrane potential assay; ROS measurement in A549 cells","journal":"Chemical research in toxicology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — covalent binding identified by targeted proteomics with multiple functional readouts, single lab, single study","pmids":["41714849"],"is_preprint":false}],"current_model":"ATP5PB (subunit b of the mitochondrial ATP synthase F0 complex) forms part of the peripheral stalk of ATP synthase, directly interacts with cardiolipin in the inner mitochondrial membrane (an interaction disrupted in diabetic heart), and its membrane domain does not contribute to the mitochondrial permeability transition pore; it can be covalently modified by electrophilic compounds at cysteine residues, leading to mitochondrial dysfunction."},"narrative":{"mechanistic_narrative":"ATP5PB (subunit b) is a component of the F0 sector of the mitochondrial ATP synthase, where it forms part of the peripheral stalk and directly contacts cardiolipin in the inner mitochondrial membrane [PMID:23872101]. In cardiac interfibrillar mitochondria this subunit b–cardiolipin interaction is lost in type 1 diabetes, coinciding with diminished ATP synthase activity, linking the lipid contact to enzyme function [PMID:23872101]. Genetic deletion of the membrane domain of subunit b in human cells preserves the calcium-triggered, cyclosporin A–sensitive permeability transition pore, establishing that this domain is dispensable for permeability transition pore formation [PMID:28784775]. Subunit b is susceptible to covalent modification at cysteine residues by reactive electrophiles such as 6PPD-quinone, and this adduction tracks with reduced respiratory chain Complex I and IV activities, lowered ATP content and membrane potential, and elevated mitochondrial ROS [PMID:41714849]. Beyond these observations, the structural and regulatory mechanisms of ATP5PB have not been further characterized in the available corpus.","teleology":[{"year":2013,"claim":"Established that subunit b makes a direct, functionally relevant contact with cardiolipin in the inner membrane and that loss of this contact accompanies reduced ATP synthase activity in disease.","evidence":"Co-immunoprecipitation/direct interaction assay between cardiolipin and ATP synthase subunits in isolated cardiac mitochondrial subpopulations, with enzymatic activity readout in type 1 diabetic mitochondria","pmids":["23872101"],"confidence":"Medium","gaps":["Single lab, correlational link between lost cardiolipin binding and reduced activity","Does not define the residues or structural interface mediating cardiolipin binding","Mechanism connecting cardiolipin loss to activity decline not resolved"]},{"year":2017,"claim":"Resolved whether the subunit b membrane domain contributes to the permeability transition pore by showing the pore's defining properties persist without it.","evidence":"CRISPR disruption generating clonal HAP1-Δb cells with calcium-triggered swelling and cyclosporin A sensitivity assays","pmids":["28784775"],"confidence":"High","gaps":["Does not address whether other ATP synthase subunits contribute to the pore","Effect of the deletion on ATP synthesis itself not the focus","Does not define the molecular identity of the pore"]},{"year":2026,"claim":"Identified subunit b cysteines as covalent targets of reactive electrophiles, linking chemical adduction to broad mitochondrial dysfunction.","evidence":"Sulfhydryl-reactive proteomics identifying 6PPD-quinone covalent targets with respiratory complex activity, ATP, membrane potential, and ROS assays in A549 cells","pmids":["41714849"],"confidence":"Medium","gaps":["Single lab, single study with correlational functional readouts","Does not establish that ATP5PB adduction is causal for the Complex I/IV deficits","Specific modified cysteine residues and downstream mechanism not mapped"]},{"year":null,"claim":"How cardiolipin binding, cysteine modification, and peripheral stalk function mechanistically integrate to regulate ATP synthase activity remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the subunit b cardiolipin interface","Causal chain from cysteine adduction to enzyme inhibition undefined","Role of subunit b in ATP synthase assembly/dimerization not characterized in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[1]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,1,2]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[1,2]}],"complexes":["mitochondrial ATP synthase (F0 complex)"],"partners":[],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P24539","full_name":"ATP synthase peripheral stalk subunit b, mitochondrial","aliases":["ATP synthase F(0) complex subunit B1, mitochondrial","ATP synthase peripheral stalk-membrane subunit b","ATP synthase proton-transporting mitochondrial F(0) complex subunit B1","ATP synthase subunit b","ATPase subunit b"],"length_aa":256,"mass_kda":28.9,"function":"Subunit b, of the mitochondrial membrane ATP synthase complex (F(1)F(0) ATP synthase or Complex V) that produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain (PubMed:37244256). ATP synthase complex consist of a soluble F(1) head domain - the catalytic core - and a membrane F(1) domain - the membrane proton channel (PubMed:37244256). These two domains are linked by a central stalk rotating inside the F(1) region and a stationary peripheral stalk (PubMed:37244256). During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation (Probable). In vivo, can only synthesize ATP although its ATP hydrolase activity can be activated artificially in vitro (By similarity). Part of the complex F(0) domain (PubMed:37244256). Part of the complex F(0) domain and the peripheric stalk, which acts as a stator to hold the catalytic alpha(3)beta(3) subcomplex and subunit a/ATP6 static relative to the rotary elements (By similarity)","subcellular_location":"Mitochondrion; Mitochondrion inner membrane","url":"https://www.uniprot.org/uniprotkb/P24539/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/ATP5PB","classification":"Common Essential","n_dependent_lines":727,"n_total_lines":1208,"dependency_fraction":0.6018211920529801},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ATP5PB","total_profiled":1310},"omim":[{"mim_id":"617228","title":"COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 31; COXPD31","url":"https://www.omim.org/entry/617228"},{"mim_id":"603270","title":"ATP SYNTHASE PERIPHERAL STALK MEMBRANE, SUBUNIT B; ATP5PB","url":"https://www.omim.org/entry/603270"},{"mim_id":"602241","title":"MITOCHONDRIAL INTERMEDIATE PEPTIDASE; MIPEP","url":"https://www.omim.org/entry/602241"},{"mim_id":"300111","title":"PRICKLE PLANAR CELL POLARITY PROTEIN 3; PRICKLE3","url":"https://www.omim.org/entry/300111"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Mitochondria","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":127.5},{"tissue":"tongue","ntpm":122.9}],"url":"https://www.proteinatlas.org/search/ATP5PB"},"hgnc":{"alias_symbol":[],"prev_symbol":["ATP5F1"]},"alphafold":{"accession":"P24539","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P24539","model_url":"https://alphafold.ebi.ac.uk/files/AF-P24539-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P24539-F1-predicted_aligned_error_v6.png","plddt_mean":83.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ATP5PB","jax_strain_url":"https://www.jax.org/strain/search?query=ATP5PB"},"sequence":{"accession":"P24539","fasta_url":"https://rest.uniprot.org/uniprotkb/P24539.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P24539/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P24539"}},"corpus_meta":[{"pmid":"23916858","id":"PMC_23916858","title":"Chinese herbal medicine-derived compounds for cancer therapy: a focus on hepatocellular 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HAP1-Δb cells, functional PTP assay (calcium-triggered swelling, cyclosporin A sensitivity)\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic knockout with defined functional readout, complemented by parallel OSCP knockout, rigorous controls, published in peer-reviewed journal\",\n      \"pmids\": [\"28784775\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"ATP5F1 (subunit b of the ATP synthase F0 complex) directly interacts with cardiolipin in cardiac interfibrillar mitochondria; this interaction is significantly decreased in type 1 diabetic interfibrillar mitochondria, coinciding with reduced ATP synthase activity.\",\n      \"method\": \"Co-immunoprecipitation/direct interaction assay between cardiolipin and ATP synthase subunits in isolated cardiac mitochondrial subpopulations; Western blot for protein content; enzymatic activity assay for ATP synthase\",\n      \"journal\": \"Life sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct interaction identified by pulldown/co-IP in isolated mitochondria with functional enzymatic activity readout, single lab\",\n      \"pmids\": [\"23872101\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"6PPDQ covalently binds to ATP5PB (subunit b of ATP synthase) via its cysteine residues, and this binding is associated with decreased Complex I and IV enzymatic activities, reduced cellular ATP content, reduced mitochondrial membrane potential, and elevated mitochondrial ROS.\",\n      \"method\": \"Sulfhydryl-reactive proteomics platform identifying covalent binding targets; enzymatic activity assays for mitochondrial respiratory chain complexes I and IV; ATP content measurement; mitochondrial membrane potential assay; ROS measurement in A549 cells\",\n      \"journal\": \"Chemical research in toxicology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — covalent binding identified by targeted proteomics with multiple functional readouts, single lab, single study\",\n      \"pmids\": [\"41714849\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ATP5PB (subunit b of the mitochondrial ATP synthase F0 complex) forms part of the peripheral stalk of ATP synthase, directly interacts with cardiolipin in the inner mitochondrial membrane (an interaction disrupted in diabetic heart), and its membrane domain does not contribute to the mitochondrial permeability transition pore; it can be covalently modified by electrophilic compounds at cysteine residues, leading to mitochondrial dysfunction.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ATP5PB (subunit b) is a component of the F0 sector of the mitochondrial ATP synthase, where it forms part of the peripheral stalk and directly contacts cardiolipin in the inner mitochondrial membrane [#1]. In cardiac interfibrillar mitochondria this subunit b–cardiolipin interaction is lost in type 1 diabetes, coinciding with diminished ATP synthase activity, linking the lipid contact to enzyme function [#1]. Genetic deletion of the membrane domain of subunit b in human cells preserves the calcium-triggered, cyclosporin A–sensitive permeability transition pore, establishing that this domain is dispensable for permeability transition pore formation [#0]. Subunit b is susceptible to covalent modification at cysteine residues by reactive electrophiles such as 6PPD-quinone, and this adduction tracks with reduced respiratory chain Complex I and IV activities, lowered ATP content and membrane potential, and elevated mitochondrial ROS [#2]. Beyond these observations, the structural and regulatory mechanisms of ATP5PB have not been further characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established that subunit b makes a direct, functionally relevant contact with cardiolipin in the inner membrane and that loss of this contact accompanies reduced ATP synthase activity in disease.\",\n      \"evidence\": \"Co-immunoprecipitation/direct interaction assay between cardiolipin and ATP synthase subunits in isolated cardiac mitochondrial subpopulations, with enzymatic activity readout in type 1 diabetic mitochondria\",\n      \"pmids\": [\"23872101\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Single lab, correlational link between lost cardiolipin binding and reduced activity\",\n        \"Does not define the residues or structural interface mediating cardiolipin binding\",\n        \"Mechanism connecting cardiolipin loss to activity decline not resolved\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Resolved whether the subunit b membrane domain contributes to the permeability transition pore by showing the pore's defining properties persist without it.\",\n      \"evidence\": \"CRISPR disruption generating clonal HAP1-\\u0394b cells with calcium-triggered swelling and cyclosporin A sensitivity assays\",\n      \"pmids\": [\"28784775\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Does not address whether other ATP synthase subunits contribute to the pore\",\n        \"Effect of the deletion on ATP synthesis itself not the focus\",\n        \"Does not define the molecular identity of the pore\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified subunit b cysteines as covalent targets of reactive electrophiles, linking chemical adduction to broad mitochondrial dysfunction.\",\n      \"evidence\": \"Sulfhydryl-reactive proteomics identifying 6PPD-quinone covalent targets with respiratory complex activity, ATP, membrane potential, and ROS assays in A549 cells\",\n      \"pmids\": [\"41714849\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Single lab, single study with correlational functional readouts\",\n        \"Does not establish that ATP5PB adduction is causal for the Complex I/IV deficits\",\n        \"Specific modified cysteine residues and downstream mechanism not mapped\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How cardiolipin binding, cysteine modification, and peripheral stalk function mechanistically integrate to regulate ATP synthase activity remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural model of the subunit b cardiolipin interface\",\n        \"Causal chain from cysteine adduction to enzyme inhibition undefined\",\n        \"Role of subunit b in ATP synthase assembly/dimerization not characterized in the corpus\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"complexes\": [\"mitochondrial ATP synthase (F0 complex)\"],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":3,"faith_total":4,"faith_pct":75.0}}