[English] 日本語
![](img/lk-miru.gif)
- PDB-7xkh: Nucleotide-depleted F1 domain of FoF1-ATPase from Bacillus PS3, state1 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7xkh | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Nucleotide-depleted F1 domain of FoF1-ATPase from Bacillus PS3, state1 | |||||||||||||||
![]() |
| |||||||||||||||
![]() | MOTOR PROTEIN / ATP synthase F1 ATPase FoF1 | |||||||||||||||
Function / homology | ![]() proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
![]() | Nakano, A. / Kishikawa, J. / Nakanishi, A. / Mitsuoka, K. / Yokoyama, K. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Structural basis of unisite catalysis of bacterial FF-ATPase. Authors: Atsuki Nakano / Jun-Ichi Kishikawa / Atsuko Nakanishi / Kaoru Mitsuoka / Ken Yokoyama / ![]() Abstract: Adenosine triphosphate (ATP) synthases (FF-ATPases) are crucial for all aerobic organisms. F, a water-soluble domain, can catalyze both the synthesis and hydrolysis of ATP with the rotation of the ...Adenosine triphosphate (ATP) synthases (FF-ATPases) are crucial for all aerobic organisms. F, a water-soluble domain, can catalyze both the synthesis and hydrolysis of ATP with the rotation of the central rotor inside a cylinder made of in three different conformations (referred to as , , and ). In this study, we determined multiple cryo-electron microscopy structures of bacterial FF exposed to different reaction conditions. The structures of nucleotide-depleted FF indicate that the ε subunit directly forces to adopt a closed form independent of the nucleotide binding to . The structure of FF under conditions that permit only a single catalytic subunit per enzyme to bind ATP is referred to as unisite catalysis and reveals that ATP hydrolysis unexpectedly occurs on instead of , where ATP hydrolysis proceeds in the steady-state catalysis of FF. This indicates that the unisite catalysis of bacterial FF significantly differs from the kinetics of steady-state turnover with continuous rotation of the shaft. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 540.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 448.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 33251MC ![]() 7xkoC ![]() 7xkpC ![]() 7xkqC ![]() 7xkrC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 54848.598 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A0M3VGF9, H+-transporting two-sector ATPase #2: Protein | Mass: 53424.625 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A0M4U1P9, H+-transporting two-sector ATPase #3: Protein | | Mass: 31859.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | | Mass: 14585.905 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #5: Chemical | ChemComp-PI / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: FoF1 from Bacillus PS3 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.53 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | 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 R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
---|---|
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9625 |
-
Processing
EM software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1381269 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201220 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6N2Y Accession code: 6N2Y / Source name: PDB / Type: experimental model |