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Open data
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Basic information
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Title | Human ATP synthase state 3a subregion 2 | |||||||||||||||
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![]() | MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() Formation of ATP by chemiosmotic coupling / Cristae formation / : / : / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / substantia nigra development / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation ...Formation of ATP by chemiosmotic coupling / Cristae formation / : / : / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / substantia nigra development / proton motive force-driven mitochondrial ATP synthesis / Mitochondrial protein degradation / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / membrane / nucleus Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.56 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 | ![]() | 483.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.2 KB 17.2 KB | Display Display | ![]() |
Images | ![]() | 60.6 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() | 475.5 MB 475.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h9nMC ![]() 8h9eC ![]() 8h9fC ![]() 8h9gC ![]() 8h9iC ![]() 8h9jC ![]() 8h9kC ![]() 8h9lC ![]() 8h9mC ![]() 8h9pC ![]() 8h9qC ![]() 8h9rC ![]() 8h9sC ![]() 8h9tC ![]() 8h9uC ![]() 8h9vC M: atomic model generated by this map C: citing same article ( |
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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
-Half map: #1
File | emd_34574_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34574_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Human ATP synthase
Entire | Name: Human ATP synthase |
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Components |
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-Supramolecule #1: Human ATP synthase
Supramolecule | Name: Human ATP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 600 KDa |
-Macromolecule #1: ATP synthase F(0) complex subunit B1, mitochondrial
Macromolecule | Name: ATP synthase F(0) complex subunit B1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.658586 KDa |
Sequence | String: PVPPLPEYGG KVRYGLIPEE FFQFLYPKTG VTGPYVLGTG LILYALSKEI YVISAETFTA LSVLGVMVYG IKKYGPFVAD FADKLNEQK LAQLEEAKQA SIQHIQNAID TEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLYRVYK EVKNRLDYHI S VQNMMRRK ...String: PVPPLPEYGG KVRYGLIPEE FFQFLYPKTG VTGPYVLGTG LILYALSKEI YVISAETFTA LSVLGVMVYG IKKYGPFVAD FADKLNEQK LAQLEEAKQA SIQHIQNAID TEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLYRVYK EVKNRLDYHI S VQNMMRRK EQEHMINWVE KHVVQSISTQ QEKETIAKCI ADLKLLAKKA QAQPVM UniProtKB: ATP synthase F(0) complex subunit B1, mitochondrial |
-Macromolecule #2: ATP synthase-coupling factor 6, mitochondrial
Macromolecule | Name: ATP synthase-coupling factor 6, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.606499 KDa |
Sequence | String: MILQRLFRFS SVIRSAVSVH LRRNIGVTAV AFNKELDPIQ KLFVDKIREY KSKRQTSGGP VDASSEYQQE LERELFKLKQ MFGNADMNT FPTFKFEDPK FEVIEKPQA UniProtKB: ATP synthase-coupling factor 6, mitochondrial |
-Macromolecule #3: ATP synthase subunit d, mitochondrial
Macromolecule | Name: ATP synthase subunit d, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 18.383982 KDa |
Sequence | String: AGRKLALKTI DWVAFAEIIP QNQKAIASSL KSWNETLTSR LAALPENPPA IDWAYYKANV AKAGLVDDFE KKFNALKVPV PEDKYTAQV DAEEKEDVKS CAEWVSLSKA RIVEYEKEME KMKNLIPFDQ MTIEDLNEAF PETKLDKKKY PYWPHQPIEN L UniProtKB: ATP synthase subunit d, mitochondrial |
-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: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45418 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |