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Yorodumi- PDB-8dbq: E. coli ATP synthase imaged in 10mM MgATP State1 "half-up" Fo cla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dbq | ||||||
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Title | E. coli ATP synthase imaged in 10mM MgATP State1 "half-up" Fo classified | ||||||
Components | (ATP synthase ...) x 9 | ||||||
Keywords | MEMBRANE PROTEIN / Energy / ATP hyrolysis / ATP synthesis / Motor / cryoEM | ||||||
Function / homology | Function and homology information proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / 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 / hydrolase activity / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Sobti, M. / Stewart, A.G. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Commun Biol / Year: 2023 Title: Changes within the central stalk of E. coli FF ATP synthase observed after addition of ATP. Authors: Meghna Sobti / Yi C Zeng / James L Walshe / Simon H J Brown / Robert Ishmukhametov / Alastair G Stewart / Abstract: FF ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F motor that is transferred to the F motor to ...FF ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F motor that is transferred to the F motor to catalyze ATP production, with flexible F/F coupling required for efficient catalysis. FF ATP synthase can also operate in reverse, hydrolyzing ATP and pumping protons, and in bacteria this function can be regulated by an inhibitory ε subunit. Here we present cryo-EM data showing E. coli FF ATP synthase in different rotational and inhibited sub-states, observed following incubation with 10 mM MgATP. Our structures demonstrate how structural transitions within the inhibitory ε subunit induce torsional movement in the central stalk, thereby enabling its rotation within the F motor. This highlights the importance of the central rotor for flexible coupling of the F and F motors and provides further insight into the regulatory mechanism mediated by subunit ε. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
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PDBx/mmCIF format | 8dbq.cif.gz | 790.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dbq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8dbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/8dbq ftp://data.pdbj.org/pub/pdb/validation_reports/db/8dbq | HTTPS FTP |
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-Related structure data
Related structure data | 27298MC 8dbpC 8dbrC 8dbsC 8dbtC 8dbuC 8dbvC 8dbwC 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 ... , 9 types, 22 molecules ACBDEFGHIJLMNOPQRSWXYa
#1: Protein | Mass: 55022.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpA, ECLG_02126 / Production host: Escherichia coli (E. coli) References: UniProt: A0A7U9G3U3, H+-transporting two-sector ATPase #2: Protein | | Mass: 54946.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpA, ECLG_02126 / Production host: Escherichia coli (E. coli) References: UniProt: A0A7U9G3U3, H+-transporting two-sector ATPase #3: Protein | Mass: 50346.129 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpD, EWT59_16525, WLH_03015 / Production host: Escherichia coli (E. coli) References: UniProt: A0A192CEZ8, H+-transporting two-sector ATPase #4: Protein | | Mass: 31237.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3SLA2 #5: Protein | | Mass: 11012.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpC, CCU01_030215 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V1DSB5 #6: Protein | Mass: 7998.754 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpE, ECJG_03465 / Production host: Escherichia coli (E. coli) / References: UniProt: F4TL55 #7: Protein | | Mass: 18855.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpH, HMPREF1611_00658 / Production host: Escherichia coli (E. coli) / References: UniProt: V0ZA15 #8: Protein | Mass: 17257.889 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpf / Production host: Escherichia coli (E. coli) / References: UniProt: D6IFY0 #9: Protein | | Mass: 29767.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3SL77 |
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-Non-polymers , 3 types, 11 molecules
#10: Chemical | ChemComp-ATP / #11: Chemical | ChemComp-MG / #12: Chemical | |
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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: ATP synthase / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
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 FIELDBright-field microscopy / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9354 / Symmetry type: POINT | ||||||||||||||||||||||||
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