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Open data
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Basic information
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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 / proton-transporting ATP synthase complex / oxidative phosphorylation / 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 / proton-transporting ATP synthase complex / oxidative phosphorylation / cellular response to interleukin-7 / response to copper ion / response to muscle activity / cellular response to nitric oxide / : / : / : / : / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial nucleoid / : / MHC class I protein binding / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / positive regulation of blood vessel endothelial cell migration / response to hyperoxia / generation of precursor metabolites and energy / proton-transporting ATP synthase complex, catalytic core F(1) / cellular response to dexamethasone stimulus / H+-transporting two-sector ATPase / substantia nigra development / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / lipid metabolic process / regulation of intracellular pH / Transcriptional activation of mitochondrial biogenesis / mitochondrial membrane / aerobic respiration / ADP binding / osteoblast differentiation / nuclear membrane / protease binding / angiogenesis / response to ethanol / mitochondrial inner membrane / mitochondrial matrix / hydrolase activity / 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 | 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 483.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.8 KB 28.8 KB | Display Display | ![]() |
Images | ![]() | 99.9 KB | ||
Filedesc metadata | ![]() | 7.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h9vMC ![]() 8h9eC ![]() 8h9fC ![]() 8h9gC ![]() 8h9iC ![]() 8h9jC ![]() 8h9kC ![]() 8h9lC ![]() 8h9mC ![]() 8h9nC ![]() 8h9pC ![]() 8h9qC ![]() 8h9rC ![]() 8h9sC ![]() 8h9tC ![]() 8h9uC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.73 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Human ATP synthase
+Supramolecule #1: Human ATP synthase
+Macromolecule #1: ATP synthase F(0) complex subunit C1, mitochondrial
+Macromolecule #2: ATP synthase subunit delta, mitochondrial
+Macromolecule #3: ATP synthase subunit epsilon, mitochondrial
+Macromolecule #4: ATP synthase F(0) complex subunit B1, mitochondrial
+Macromolecule #5: ATP synthase subunit d, mitochondrial
+Macromolecule #6: ATP synthase subunit a
+Macromolecule #7: ATP synthase subunit ATP5MJ, mitochondrial
+Macromolecule #8: ATP synthase protein 8
+Macromolecule #9: ATP synthase subunit f, mitochondrial
+Macromolecule #10: ATP synthase subunit g, mitochondrial
+Macromolecule #11: ATP synthase subunit e, mitochondrial
+Macromolecule #12: ATP synthase-coupling factor 6, mitochondrial
+Macromolecule #13: ATP synthase subunit alpha, mitochondrial
+Macromolecule #14: ATP synthase subunit beta, mitochondrial
+Macromolecule #15: ATP synthase subunit gamma, mitochondrial
+Macromolecule #16: ATP synthase subunit O, mitochondrial
+Macromolecule #17: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #18: MAGNESIUM ION
+Macromolecule #19: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: AlphaFold |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23272 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |