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Yorodumi- PDB-7xko: F1 domain of epsilon C-terminal domain deleted FoF1 from Bacillus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xko | |||||||||||||||
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Title | F1 domain of epsilon C-terminal domain deleted FoF1 from Bacillus PS3,state1,nucleotide depeleted | |||||||||||||||
Components |
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Keywords | MOTOR PROTEIN / ATP synthase F1 ATPase FoF1 | |||||||||||||||
Function / homology | Function and homology information 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 | Bacillus sp. PS3 (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
Authors | Nakano, A. / Kishikawa, J. / Nakanishi, A. / Mitsuoka, K. / Yokoyama, K. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: PNAS Nexus / Year: 2022 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xko.cif.gz | 520.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xko.ent.gz | 431.9 KB | Display | PDB format |
PDBx/mmJSON format | 7xko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xko_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7xko_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7xko_validation.xml.gz | 91 KB | Display | |
Data in CIF | 7xko_validation.cif.gz | 138.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/7xko ftp://data.pdbj.org/pub/pdb/validation_reports/xk/7xko | HTTPS FTP |
-Related structure data
Related structure data | 33258MC 7xkhC 7xkpC 7xkqC 7xkrC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 54848.598 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: uncA, atpA / Production host: Escherichia coli K-12 (bacteria) 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.) Bacillus sp. PS3 (bacteria) / Gene: uncD, atpD / Production host: Escherichia coli K-12 (bacteria) 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.) Bacillus sp. PS3 (bacteria) / Gene: uncG, atpG / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0M4TPJ7 #4: Chemical | ChemComp-PI / | 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 |
-Sample preparation
Component | Name: FoF1 from Bacillus PS3 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 0.53 MDa / Experimental value: NO |
Source (natural) | Organism: Bacillus sp. PS3 (bacteria) |
Source (recombinant) | Organism: Escherichia coli K-12 (bacteria) |
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: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 0.001956 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: 7329 |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 499788 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34672 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |