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- PDB-5t4o: Autoinhibited E. coli ATP synthase state 1 -

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Basic information

Entry
Database: PDB / ID: 5t4o
TitleAutoinhibited E. coli ATP synthase state 1
Components(ATP synthase ...) x 8
KeywordsHYDROLASE / 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
ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit a / ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit delta / ATP synthase subunit c / ATP synthase epsilon chain ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit a / ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit delta / ATP synthase subunit c / ATP synthase epsilon chain / ATP synthase subunit a / ATP synthase subunit b / ATP synthase subunit b / ATP synthase subunit delta / ATP synthase gamma chain / ATP synthase subunit alpha / ATP synthase subunit beta / ATP synthase subunit c
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsSobti, M. / Smits, C. / Wong, A.S.W. / Ishmukhametov, R. / Stock, D. / Sandin, S. / Stewart, A.G.
CitationJournal: 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
DepositionAug 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / em_image_scans / Item: _citation.title
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase gamma chain
H: ATP synthase epsilon chain
I: ATP synthase subunit b
J: ATP synthase subunit b
K: ATP synthase subunit a
L: ATP synthase subunit delta
M: ATP synthase subunit c
N: ATP synthase subunit c
O: ATP synthase subunit c
P: ATP synthase subunit c
Q: ATP synthase subunit c
R: ATP synthase subunit c
S: ATP synthase subunit c
T: ATP synthase subunit c
U: ATP synthase subunit c
V: ATP synthase subunit c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)535,44226
Polymers533,49322
Non-polymers1,9494
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase ... , 8 types, 22 molecules ABCDEFGHIJKLMNOPQRSTUV

#1: Protein ATP synthase subunit alpha / / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


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 ATP synthase subunit beta / / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


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 ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


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 ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


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 ATP synthase subunit b / / ATP synthase F(0) sector subunit b / ATPase subunit I / F-type ATPase subunit b / F-ATPase subunit b


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 ATP synthase subunit a / / ATP synthase F0 sector subunit a / F-ATPase subunit 6


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 ATP synthase subunit delta / / ATP synthase F(1) sector subunit delta / F-type ATPase subunit delta / F-ATPase subunit delta


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
ATP synthase subunit c / / ATP synthase F(0) sector subunit c / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding 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 ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#10: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ATP synthase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.558 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 29 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95345 / Symmetry type: POINT

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