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- PDB-8gxz: 1 sulfate and 1 ATP bound V1EG of V/A-ATPase from Thermus thermop... -
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Basic information
Entry | Database: PDB / ID: 8gxz | ||||||||||||||||||
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Title | 1 sulfate and 1 ATP bound V1EG of V/A-ATPase from Thermus thermophilus. | ||||||||||||||||||
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![]() | HYDROLASE / rotary ATPase / V/A-type ATPase / V-ATPase. | ||||||||||||||||||
Function / homology | ![]() proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / plant-type vacuole / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / fungal-type vacuole membrane / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism ...proton-transporting two-sector ATPase complex, catalytic domain / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / plant-type vacuole / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / fungal-type vacuole membrane / H+-transporting two-sector ATPase / phagocytic vesicle / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / lysosomal membrane / ATP binding / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
![]() | Nakanishi, A. / Kishikawa, J. / Mitsuoka, K. / Yokoyama, K. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding. Authors: Atsuko Nakanishi / Jun-Ichi Kishikawa / Kaoru Mitsuoka / Ken Yokoyama / ![]() Abstract: Vacuolar/archaeal-type ATPase (V/A-ATPase) is a rotary ATPase that shares a common rotary catalytic mechanism with FF ATP synthase. Structural images of V/A-ATPase obtained by single-particle cryo- ...Vacuolar/archaeal-type ATPase (V/A-ATPase) is a rotary ATPase that shares a common rotary catalytic mechanism with FF ATP synthase. Structural images of V/A-ATPase obtained by single-particle cryo-electron microscopy during ATP hydrolysis identified several intermediates, revealing the rotary mechanism under steady-state conditions. However, further characterization is needed to understand the transition from the ground state to the steady state. Here, we identified the cryo-electron microscopy structures of V/A-ATPase corresponding to short-lived initial intermediates during the activation of the ground state structure by time-resolving snapshot analysis. These intermediate structures provide insights into how the ground-state structure changes to the active, steady state through the sequential binding of ATP to its three catalytic sites. All the intermediate structures of V/A-ATPase adopt the same asymmetric structure, whereas the three catalytic dimers adopt different conformations. This is significantly different from the initial activation process of FF, where the overall structure of the F domain changes during the transition from a pseudo-symmetric to a canonical asymmetric structure (PNAS NEXUS, pgac116, 2022). In conclusion, our findings provide dynamical information that will enhance the future prospects for studying the initial activation processes of the enzymes, which have unknown intermediate structures in their functional pathway. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 720.7 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 34366MC ![]() 8gxuC ![]() 8gxwC ![]() 8gxxC ![]() 8gxyC 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
-V-type ATP synthase ... , 5 types, 10 molecules ABCDEFGHJL
#1: Protein | Mass: 63669.957 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: Authors state that the bacterium they used has two mutations in its genome (S232A and T235S) and they obtained the EM sample from Natural source. Source: (natural) ![]() ![]() References: UniProt: Q56403, H+-transporting two-sector ATPase #2: Protein | Mass: 53219.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | | Mass: 24715.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | | Mass: 11294.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 20645.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 1 types, 2 molecules IK
#5: Protein | Mass: 13166.218 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 3 types, 3 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
#7: Chemical | ChemComp-SO4 / |
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#8: Chemical | ChemComp-ATP / |
#9: Chemical | ChemComp-MG / |
-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: 1 sulfate and 1 ATP bound V1EG of V/A-ATPase from Thermus thermophilus Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL |
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Molecular weight | Value: 0.6 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: MOLYBDENUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20rc4_4425: / Classification: refinement | ||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39101 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7VAL Accession code: 7VAL / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||
Refine LS restraints |
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