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- PDB-5y5y: V/A-type ATPase/synthase from Thermus thermophilus, peripheral do... -
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Basic information
Entry | Database: PDB / ID: 5y5y | |||||||||
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Title | V/A-type ATPase/synthase from Thermus thermophilus, peripheral domain, rotational state 1 | |||||||||
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![]() | MOTOR PROTEIN / ATP synthase / proton pump / V-ATPase / Bioenergetics | |||||||||
Function / homology | ![]() proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / plant-type vacuole / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / vacuolar acidification / fungal-type vacuole membrane / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / phagocytic vesicle ...proton-transporting V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / plant-type vacuole / vacuolar proton-transporting V-type ATPase complex / proton-transporting ATP synthase complex / vacuolar acidification / fungal-type vacuole membrane / proton motive force-driven plasma membrane ATP synthesis / 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: 4.7 Å | |||||||||
![]() | Nakanishi, A. / Kishikawa, J. / Tamakoshi, M. / Mitsuoka, K. / Yokoyama, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo EM structure of intact rotary H-ATPase/synthase from Thermus thermophilus. Authors: Atsuko Nakanishi / Jun-Ichi Kishikawa / Masatada Tamakoshi / Kaoru Mitsuoka / Ken Yokoyama / ![]() Abstract: Proton translocating rotary ATPases couple ATP hydrolysis/synthesis, which occurs in the soluble domain, with proton flow through the membrane domain via a rotation of the common central rotor ...Proton translocating rotary ATPases couple ATP hydrolysis/synthesis, which occurs in the soluble domain, with proton flow through the membrane domain via a rotation of the common central rotor complex against the surrounding peripheral stator apparatus. Here, we present a large data set of single particle cryo-electron micrograph images of the V/A type H-rotary ATPase from the bacterium Thermus thermophilus, enabling the identification of three rotational states based on the orientation of the rotor subunit. Using masked refinement and classification with signal subtractions, we obtain homogeneous reconstructions for the whole complexes and soluble V domains. These reconstructions are of higher resolution than any EM map of intact rotary ATPase reported previously, providing a detailed molecular basis for how the rotary ATPase maintains structural integrity of the peripheral stator apparatus, and confirming the existence of a clear proton translocation path from both sides of the membrane. | |||||||||
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 | ![]() | 690.5 KB | Display | ![]() |
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PDB format | ![]() | 559.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 114.3 KB | Display | |
Data in CIF | ![]() | 175.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6811MC ![]() 6810C ![]() 6812C ![]() 6813C ![]() 5y5xC ![]() 5y5zC ![]() 5y60C 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 ABCDEFGHJLM
#1: Protein | Mass: 63699.980 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: 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: 20699.693 Da / Num. of mol.: 2 / 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 / Non-polymers , 2 types, 4 molecules IK![](data/chem/img/ADP.gif)
![](data/chem/img/ADP.gif)
#5: Protein | Mass: 13166.218 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Chemical | |
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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: V/A-type ATPase/synthase from Thermus thermophilus, peripheral domai, rotational state 1. Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Value: 0.65 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.027 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: MOLYBDENUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 26 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Movie frames/image: 7 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117938 / Symmetry type: POINT |