+Open data
-Basic information
Entry | Database: PDB / ID: 7l1q | ||||||
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Title | PS3 F1-ATPase Binding/TS Dwell | ||||||
Components |
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Keywords | TRANSLOCASE / ATPase / ATP synthase | ||||||
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. (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Sobti, M. / Ueno, H. / Noji, H. / Stewart, A.G. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: The six steps of the complete F-ATPase rotary catalytic cycle. Authors: Meghna Sobti / Hiroshi Ueno / Hiroyuki Noji / Alastair G Stewart / Abstract: FF ATP synthase interchanges phosphate transfer energy and proton motive force via a rotary catalysis mechanism. Isolated F-ATPase catalytic cores can hydrolyze ATP, passing through six intermediate ...FF ATP synthase interchanges phosphate transfer energy and proton motive force via a rotary catalysis mechanism. Isolated F-ATPase catalytic cores can hydrolyze ATP, passing through six intermediate conformational states to generate rotation of their central γ-subunit. Although previous structural studies have contributed greatly to understanding rotary catalysis in the F-ATPase, the structure of an important conformational state (the binding-dwell) has remained elusive. Here, we exploit temperature and time-resolved cryo-electron microscopy to determine the structure of the binding- and catalytic-dwell states of Bacillus PS3 F-ATPase. Each state shows three catalytic β-subunits in different conformations, establishing the complete set of six states taken up during the catalytic cycle and providing molecular details for both the ATP binding and hydrolysis strokes. We also identify a potential phosphate-release tunnel that indicates how ADP and phosphate binding are coordinated during synthesis. Overall these findings provide a structural basis for the entire F-ATPase catalytic cycle. | ||||||
History |
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-Structure visualization
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Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7l1q.cif.gz | 531.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l1q.ent.gz | 435.2 KB | Display | PDB format |
PDBx/mmJSON format | 7l1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7l1q_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7l1q_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7l1q_validation.xml.gz | 80.6 KB | Display | |
Data in CIF | 7l1q_validation.cif.gz | 121.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/7l1q ftp://data.pdbj.org/pub/pdb/validation_reports/l1/7l1q | HTTPS FTP |
-Related structure data
Related structure data | 23115MC 7l1rC 7l1sC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-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: 55881.676 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (strain PS3) (bacteria) / Strain: PS3 / Gene: uncA, atpA / Production host: Escherichia coli (E. coli) References: UniProt: A0A0M3VGF9, H+-transporting two-sector ATPase #2: Protein | Mass: 53410.602 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (strain PS3) (bacteria) / Strain: PS3 / Gene: uncD, atpD / Production host: Escherichia coli (E. coli) References: UniProt: A0A0M4U1P9, H+-transporting two-sector ATPase |
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-Protein , 1 types, 1 molecules G
#3: Protein | Mass: 31865.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (strain PS3) (bacteria) / Strain: PS3 / Gene: uncG, atpG / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4TPJ7 |
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-Non-polymers , 4 types, 13 molecules
#4: Chemical | ChemComp-ATP / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-ADP / | #7: Chemical | ChemComp-PO4 / | |
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-Details
Has ligand of interest | N |
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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: PS3 F1-ATPase Binding/TS Dwell / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Bacillus sp. (strain PS3) (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
Specimen | 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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 482550 / Symmetry type: POINT | ||||||||||||||||||||||||
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