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Open data
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Basic information
Entry | Database: PDB / ID: 5gas | ||||||
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Title | Thermus thermophilus V/A-ATPase, conformation 2 | ||||||
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![]() | HYDROLASE / V/A-ATPase / V-ATPase / A-ATPase / Thermus thermophilus / rotary ATPase / membrane protein | ||||||
Function / homology | ![]() proton-transporting V-type ATPase, V0 domain / 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 V-type ATPase, V0 domain / 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 / ATPase binding / lysosomal membrane / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å | ||||||
![]() | Schep, D.G. / Zhao, J. / Rubinstein, J.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance. Authors: Daniel G Schep / Jianhua Zhao / John L Rubinstein / ![]() Abstract: Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the ...Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the membrane-embedded a subunit. The V/A-ATPase from the eubacterium Thermus thermophilus is similar in structure to the eukaryotic V-ATPase but has a simpler subunit composition and functions in vivo to synthesize ATP rather than pump protons. We determined the T. thermophilus V/A-ATPase structure by cryo-EM at 6.4 Å resolution. Evolutionary covariance analysis allowed tracing of the a subunit sequence within the map, providing a complete model of the rotary ATPase. Comparing the membrane-embedded regions of the T. thermophilus V/A-ATPase and eukaryotic V-ATPase from Saccharomyces cerevisiae allowed identification of the α-helices that belong to the a subunit and revealed the existence of previously unknown subunits in the eukaryotic enzyme. Subsequent evolutionary covariance analysis enabled construction of a model of the a subunit in the S. cerevisae V-ATPase that explains numerous biochemical studies of that enzyme. Comparing the two a subunit structures determined here with a structure of the distantly related a subunit from the bovine F-type ATP synthase revealed a conserved pattern of residues, suggesting a common mechanism for proton transport in all rotary ATPases. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 696.7 KB | Display | ![]() |
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PDB format | ![]() | 427.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8017MC ![]() 8016C ![]() 8070C ![]() 5garC ![]() 5i1mC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-V-type ATP synthase ... , 6 types, 11 molecules ABCDEFGHKLM
#1: Protein | Mass: 63628.902 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q56403, H+-transporting two-sector ATPase #2: Protein | Mass: 50850.738 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 20481.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | | Mass: 23350.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | | Mass: 10824.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | | Mass: 35968.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 3 types, 15 molecules IJNOPQRSTUVWXYZ
#4: Protein | Mass: 11752.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | | Mass: 72272.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 9841.714 Da / Num. of mol.: 12 / 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: Intact Thermus thermophilus V/A-ATPase / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Homemade nanofabricated 400 mesh copper/rhodium grid Grid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: Homemade nanofabricated |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K Details: Plunged into liquid ethane/propane (FEI VITROBOT MARK III). |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 34483 X / Nominal defocus max: 6000 nm / Nominal defocus min: 1000 nm / Cs: 2 mm / C2 aperture diameter: 30 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Image recording | Average exposure time: 15 sec. / Electron dose: 35.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 12 |
Image scans | Movie frames/image: 30 / Used frames/image: 1-30 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9721 / Symmetry type: POINT |