+Open data
-Basic information
Entry | Database: PDB / ID: 8h9l | |||||||||||||||
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Title | Human ATP synthase F1 domain, state 3a | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / regulation of protein targeting to mitochondrion / negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / positive regulation of proteolysis involved in protein catabolic process / Cristae formation / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / ATP biosynthetic process / angiostatin binding ...mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / regulation of protein targeting to mitochondrion / negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / positive regulation of proteolysis involved in protein catabolic process / Cristae formation / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / ATP biosynthetic process / angiostatin binding / mitochondrial depolarization / ATPase inhibitor activity / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / Mitochondrial protein import / negative regulation of ATP-dependent activity / negative regulation of hydrolase activity / oxidative phosphorylation / proton-transporting ATP synthase complex / cellular response to interleukin-7 / enzyme inhibitor activity / response to muscle activity / mitochondrial proton-transporting ATP synthase, stator stalk / heme biosynthetic process / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / mitochondrial proton-transporting ATP synthase complex / negative regulation of endothelial cell proliferation / MHC class I protein binding / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / cellular response to nitric oxide / positive regulation of blood vessel endothelial cell migration / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton transmembrane transport / reactive oxygen species metabolic process / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / erythrocyte differentiation / cellular response to dexamethasone stimulus / generation of precursor metabolites and energy / mitochondrial membrane / regulation of intracellular pH / Transcriptional activation of mitochondrial biogenesis / lipid metabolic process / ADP binding / osteoblast differentiation / ATPase binding / angiogenesis / response to ethanol / protease binding / mitochondrial inner membrane / calmodulin binding / mitochondrial matrix / membrane raft / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å | |||||||||||||||
Authors | Lai, Y. / Zhang, Y. / Liu, F. / Gao, Y. / Gong, H. / Rao, Z. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Mol Cell / Year: 2023 Title: Structure of the human ATP synthase. Authors: Yuezheng Lai / Yuying Zhang / Shan Zhou / Jinxu Xu / Zhanqiang Du / Ziyan Feng / Long Yu / Ziqing Zhao / Weiwei Wang / Yanting Tang / Xiuna Yang / Luke W Guddat / Fengjiang Liu / Yan Gao / ...Authors: Yuezheng Lai / Yuying Zhang / Shan Zhou / Jinxu Xu / Zhanqiang Du / Ziyan Feng / Long Yu / Ziqing Zhao / Weiwei Wang / Yanting Tang / Xiuna Yang / Luke W Guddat / Fengjiang Liu / Yan Gao / Zihe Rao / Hongri Gong / Abstract: Biological energy currency ATP is produced by FF-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main ...Biological energy currency ATP is produced by FF-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase using cryoelectron microscopy. These structures reveal that the release of ADP occurs when the β subunit of FF-ATP synthase is in the open conformation, showing how ADP binding is coordinated during synthesis. The accommodation of the symmetry mismatch between F and F motors is resolved by the torsional flexing of the entire complex, especially the γ subunit, and the rotational substep of the c subunit. Water molecules are identified in the inlet and outlet half-channels, suggesting that the proton transfer in these two half-channels proceed via a Grotthus mechanism. Clinically relevant mutations are mapped to the structure, showing that they are mainly located at the subunit-subunit interfaces, thus causing instability of the complex. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h9l.cif.gz | 520.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h9l.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8h9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/8h9l ftp://data.pdbj.org/pub/pdb/validation_reports/h9/8h9l | HTTPS FTP |
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-Related structure data
Related structure data | 34572MC 8h9eC 8h9fC 8h9gC 8h9iC 8h9jC 8h9kC 8h9mC 8h9nC 8h9pC 8h9qC 8h9rC 8h9sC 8h9tC 8h9uC 8h9vC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-ATP synthase subunit ... , 4 types, 8 molecules ABCEFDGO
#1: Protein | Mass: 55276.160 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25705 #2: Protein | Mass: 51821.965 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P06576, H+-transporting two-sector ATPase #3: Protein | | Mass: 30207.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36542 #5: Protein | | Mass: 20904.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48047 |
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-Protein , 1 types, 1 molecules J
#4: Protein | Mass: 9540.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UII2 |
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-Non-polymers , 3 types, 10 molecules
#6: Chemical | #7: Chemical | ChemComp-MG / #8: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human ATP synthase / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL |
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Molecular weight | Value: 0.6 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
EM imaging optics | Energyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45418 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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