+Open data
-Basic information
Entry | Database: PDB / ID: 8hh5 | |||||||||||||||
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Title | F1 domain of FoF1-ATPase from Bacillus PS3,120 degrees,highATP | |||||||||||||||
Components |
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Keywords | TRANSLOCASE/MOTOR PROTEIN / ATP synthase F1 ATPase FoF1 / MOTOR PROTEIN / TRANSLOCASE-MOTOR PROTEIN complex | |||||||||||||||
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: 2.9 Å | |||||||||||||||
Authors | Nakano, A. / Kishikawa, J. / Mitsuoka, K. / Yokoyama, K. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: To Be Published Title: Rotation mechanism of ATP synthases driven by ATP hydrolysis Authors: Nakano, A. / Yokoyama, K. / Kishikawa, J. / Nakanishi, A. / Mitsuoka, K. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hh5.cif.gz | 528.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hh5.ent.gz | 436.1 KB | Display | PDB format |
PDBx/mmJSON format | 8hh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hh5_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 8hh5_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 8hh5_validation.xml.gz | 92.8 KB | Display | |
Data in CIF | 8hh5_validation.cif.gz | 139.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/8hh5 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/8hh5 | HTTPS FTP |
-Related structure data
Related structure data | 34752MC 8hh1C 8hh2C 8hh3C 8hh4C 8hh6C 8hh7C 8hh8C 8hh9C 8hhaC 8hhbC 8hhcC 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
-ATP synthase subunit ... , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 54717.398 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 |
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-Protein , 1 types, 1 molecules G
#3: Protein | Mass: 31728.328 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 |
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-Non-polymers , 4 types, 13 molecules
#4: Chemical | ChemComp-ATP / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-ADP / | |
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-Details
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 | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: 0.03843 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5922 |
-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: 1118093 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14694 / Algorithm: FOURIER SPACE / 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 |