+Open data
-Basic information
Entry | Database: PDB / ID: 5gas | ||||||
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Title | Thermus thermophilus V/A-ATPase, conformation 2 | ||||||
Components |
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Keywords | HYDROLASE / V/A-ATPase / V-ATPase / A-ATPase / Thermus thermophilus / rotary ATPase / membrane protein | ||||||
Function / homology | Function and homology information proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å | ||||||
Authors | Schep, D.G. / Zhao, J. / Rubinstein, J.L. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2016 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5gas.cif.gz | 696.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gas.ent.gz | 427.7 KB | Display | PDB format |
PDBx/mmJSON format | 5gas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gas_validation.pdf.gz | 965.3 KB | Display | wwPDB validaton report |
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Full document | 5gas_full_validation.pdf.gz | 991.4 KB | Display | |
Data in XML | 5gas_validation.xml.gz | 112 KB | Display | |
Data in CIF | 5gas_validation.cif.gz | 197.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/5gas ftp://data.pdbj.org/pub/pdb/validation_reports/ga/5gas | HTTPS FTP |
-Related structure data
Related structure data | 8017MC 8016C 8070C 5garC 5i1mC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-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) Thermus thermophilus (bacteria) / Strain: AH8 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) Thermus thermophilus (bacteria) / Strain: AH8 / References: UniProt: Q72J73, UniProt: Q56404*PLUS #3: Protein | Mass: 20481.418 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: AH8 / References: UniProt: P74901 #5: Protein | | Mass: 23350.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: AH8 / References: UniProt: Q72J74, UniProt: O87880*PLUS #6: Protein | | Mass: 10824.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: AH8 / References: UniProt: P74903 #7: Protein | | Mass: 35968.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: AH8 / References: UniProt: P74902 |
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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) Thermus thermophilus (bacteria) / Strain: AH8 / References: UniProt: Q72J66, UniProt: Q5SIT5*PLUS #8: Protein | | Mass: 72272.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: AH8 / References: UniProt: H9ZQR4 #9: Protein | Mass: 9841.714 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: AH8 / References: UniProt: P74900, UniProt: Q5SIT7*PLUS |
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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 |
-Sample preparation
Component | Name: Intact Thermus thermophilus V/A-ATPase / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Thermus thermophilus (bacteria) / Strain: AH8 |
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). |
-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: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
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 |
-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 |