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Open data
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Basic information
Entry | Database: PDB / ID: 8h9v | |||||||||||||||
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Title | Human ATP synthase state 3b (combined) | |||||||||||||||
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![]() | MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / angiostatin binding / Mitochondrial protein import / mitochondrial proton-transporting ATP synthase complex assembly / oxidative phosphorylation / proton-transporting ATP synthase complex / cellular response to interleukin-7 ...negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / angiostatin binding / Mitochondrial protein import / mitochondrial proton-transporting ATP synthase complex assembly / oxidative phosphorylation / proton-transporting ATP synthase complex / cellular response to interleukin-7 / response to muscle activity / response to copper ion / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial nucleoid / mitochondrial proton-transporting ATP synthase complex / MHC class I protein binding / negative regulation of endothelial cell proliferation / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton motive force-driven mitochondrial ATP synthesis / cellular response to nitric oxide / response to hyperoxia / 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 / Mitochondrial protein degradation / substantia nigra development / aerobic respiration / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / 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 / nuclear membrane / angiogenesis / response to ethanol / protease binding / mitochondrial inner membrane / hydrolase activity / mitochondrial matrix / membrane raft / lipid binding / cell surface / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å | |||||||||||||||
![]() | Lai, Y. / Zhang, Y. / Liu, F. / Gao, Y. / Gong, H. / Rao, Z. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 829.2 KB | Display | ![]() |
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PDB format | ![]() | 683.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 127.4 KB | Display | |
Data in CIF | ![]() | 195.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34583MC ![]() 8h9eC ![]() 8h9fC ![]() 8h9gC ![]() 8h9iC ![]() 8h9jC ![]() 8h9kC ![]() 8h9lC ![]() 8h9mC ![]() 8h9nC ![]() 8h9pC ![]() 8h9qC ![]() 8h9rC ![]() 8h9sC ![]() 8h9tC ![]() 8h9uC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-ATP synthase F(0) complex subunit ... , 2 types, 9 molecules 45678123K
#1: Protein | Mass: 7610.954 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | | Mass: 24658.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-ATP synthase subunit ... , 12 types, 16 molecules HIMNPRSTABCEFDGO
#2: Protein | Mass: 15029.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
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#3: Protein | Mass: 5790.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
#5: Protein | Mass: 18383.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
#6: Protein | Mass: 24833.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
#7: Protein | Mass: 6673.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
#9: Protein | Mass: 10804.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
#10: Protein | Mass: 11309.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
#11: Protein | Mass: 7947.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||
#13: Protein | Mass: 55276.160 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | Mass: 51821.965 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P06576, H+-transporting two-sector ATPase #15: Protein | | Mass: 30207.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #16: Protein | | Mass: 20904.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 2 types, 2 molecules QL
#8: Protein | Mass: 8000.634 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#12: Protein | Mass: 12606.499 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 3 types, 10 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
#17: Chemical | #18: Chemical | ChemComp-MG / #19: 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 |
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Sample preparation
Component | Name: Human ATP synthase / Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL |
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Molecular weight | Value: 0.6 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / 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 |
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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: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23272 / Symmetry type: POINT | ||||||||||||||||||||||||
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