+Open data
-Basic information
Entry | Database: PDB / ID: 5t4q | ||||||
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Title | Autoinhibited E. coli ATP synthase state 3 | ||||||
Components | (ATP synthase ...) x 8 | ||||||
Keywords | HYDROLASE / ATP synthase / ATPase / rotary motor / membrane protein | ||||||
Function / homology | Function and homology information proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven 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 / lipid binding ...proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven 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 / lipid binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.53 Å | ||||||
Authors | Sobti, M. / Smits, C. / Wong, A.S.W. / Ishmukhametov, R. / Stock, D. / Sandin, S. / Stewart, A.G. | ||||||
Citation | Journal: Elife / Year: 2016 Title: Cryo-EM structures of the autoinhibited ATP synthase in three rotational states. Authors: Meghna Sobti / Callum Smits / Andrew Sw Wong / Robert Ishmukhametov / Daniela Stock / Sara Sandin / Alastair G Stewart / Abstract: A molecular model that provides a framework for interpreting the wealth of functional information obtained on the F-ATP synthase has been generated using cryo-electron microscopy. Three different ...A molecular model that provides a framework for interpreting the wealth of functional information obtained on the F-ATP synthase has been generated using cryo-electron microscopy. Three different states that relate to rotation of the enzyme were observed, with the central stalk's ε subunit in an extended autoinhibitory conformation in all three states. The F motor comprises of seven transmembrane helices and a decameric c-ring and invaginations on either side of the membrane indicate the entry and exit channels for protons. The proton translocating subunit contains near parallel helices inclined by ~30° to the membrane, a feature now synonymous with rotary ATPases. For the first time in this rotary ATPase subtype, the peripheral stalk is resolved over its entire length of the complex, revealing the F attachment points and a coiled-coil that bifurcates toward the membrane with its helices separating to embrace subunit from two sides. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5t4q.cif.gz | 680.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t4q.ent.gz | 479.1 KB | Display | PDB format |
PDBx/mmJSON format | 5t4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t4q_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5t4q_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5t4q_validation.xml.gz | 98.4 KB | Display | |
Data in CIF | 5t4q_validation.cif.gz | 164.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/5t4q ftp://data.pdbj.org/pub/pdb/validation_reports/t4/5t4q | HTTPS FTP |
-Related structure data
Related structure data | 8359MC 8357C 8358C 5t4oC 5t4pC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-ATP synthase ... , 8 types, 22 molecules ABCDEFGHIJKLMNOPQRSTUV
#1: Protein | Mass: 55138.531 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpA, ECS88_4156 / Production host: Escherichia coli (E. coli) References: UniProt: B7MGF4, UniProt: P0ABB0*PLUS, H+-transporting two-sector ATPase #2: Protein | Mass: 51664.574 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpD, ECS88_4154 / Production host: Escherichia coli (E. coli) References: UniProt: B7MGF2, UniProt: P0ABB4*PLUS, H+-transporting two-sector ATPase #3: Protein | | Mass: 31539.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpG, ECS88_4155 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGF3, UniProt: P0ABA6*PLUS #4: Protein | | Mass: 15087.244 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpC, ECS88_4153 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGF1, UniProt: P0A6E6*PLUS #5: Protein | Mass: 17126.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpF, Z5234, ECs4678 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABA2, UniProt: P0ABA0*PLUS #6: Protein | | Mass: 30324.096 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpB, EC55989_4213 / Production host: Escherichia coli (E. coli) / References: UniProt: B7L888, UniProt: P0AB98*PLUS #7: Protein | | Mass: 19289.061 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpH, ECS88_4157 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGF5, UniProt: P0ABA4*PLUS #8: Protein | Mass: 8259.064 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpE, ECIAI39_4341 / Production host: Escherichia coli (E. coli) / References: UniProt: B7NR39, UniProt: P68699*PLUS |
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-Non-polymers , 2 types, 4 molecules
#9: Chemical | #10: Chemical | ChemComp-ADP / | |
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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: ATP synthase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.558 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Plasmid: pFV2 |
Buffer solution | pH: 8 |
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: 29 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 8.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95345 / Symmetry type: POINT |