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Open data
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Basic information
Entry | Database: PDB / ID: 8h9j | |||||||||||||||
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Title | Human ATP synthase state2 subregion 3 | |||||||||||||||
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![]() | MEMBRANE PROTEIN / ATP synthase | |||||||||||||||
Function / homology | ![]() Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / Mitochondrial protein import / mitochondrial proton-transporting ATP synthase complex assembly / oxidative phosphorylation / response to copper ion / : / : / : ...Formation of ATP by chemiosmotic coupling / Cristae formation / ATP biosynthetic process / Mitochondrial protein import / mitochondrial proton-transporting ATP synthase complex assembly / oxidative phosphorylation / response to copper ion / : / : / : / proton-transporting ATP synthase complex, coupling factor F(o) / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / response to hyperoxia / substantia nigra development / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / aerobic respiration / nuclear membrane / mitochondrial inner membrane / mitochondrial matrix / hydrolase activity / lipid binding / mitochondrion / RNA binding / membrane / nucleus Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 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 | ![]() | 282.7 KB | Display | ![]() |
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PDB format | ![]() | 223.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 34569MC ![]() 8h9eC ![]() 8h9fC ![]() 8h9gC ![]() 8h9iC ![]() 8h9kC ![]() 8h9lC ![]() 8h9mC ![]() 8h9nC ![]() 8h9pC ![]() 8h9qC ![]() 8h9rC ![]() 8h9sC ![]() 8h9tC ![]() 8h9uC ![]() 8h9vC 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 67812345K
#1: Protein | Mass: 7610.954 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() #5: 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 ... , 9 types, 9 molecules GHIMNPRST
#2: Protein | Mass: 30207.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#3: Protein | Mass: 15029.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 5790.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 18383.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 24833.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: 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) ![]() |
-Protein , 1 types, 1 molecules Q
#12: Protein | Mass: 8000.634 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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: all / 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: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37480 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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