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- PDB-5t4q: Autoinhibited E. coli ATP synthase state 3 -

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Entry
Database: PDB / ID: 5t4q
TitleAutoinhibited E. coli ATP synthase state 3
Descriptor(ATP synthase ...) x 8
KeywordsHYDROLASE / ATP synthase / ATPase / rotary motor / membrane protein
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (8.53 Å resolution / Particle / Single particle)
AuthorsSobti, M. / Smits, C. / Wong, A.S.W. / Ishmukhametov, R. / Stock, D. / Sandin, S. / Stewart, A.G.
CitationElife, 2016, 5

Elife, 2016, 5 StrPapers
Cryo-EM structures of the autoinhibited E. coli ATP synthase in three rotational states.
Meghna Sobti / Callum Smits / Andrew Sw Wong / Robert Ishmukhametov / Daniela Stock / Sara Sandin / Alastair G Stewart

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 29, 2016 / Release: Jan 4, 2017

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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
Polyers533,49322
Non-polymers1,9494
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Polypeptide(L)ATP synthase subunit alpha / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 55138.531 Da / Num. of mol.: 3 / Source: (gene. exp.) Escherichia coli / References: UniProt: B7MGF4, EC: 3.6.3.14

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)ATP synthase subunit beta / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 51664.574 Da / Num. of mol.: 3 / Source: (gene. exp.) Escherichia coli / References: UniProt: B7MGF2, EC: 3.6.3.14

Cellular component

Molecular function

  • ATP binding (GO: 0005524)
  • proton-transporting ATP synthase activity, rotational mechanism (GO: 0046933)
  • proton-transporting ATPase activity, rotational mechanism (GO: 0046961)

Biological process

#3: Polypeptide(L)ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 31539.285 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: B7MGF3

Cellular component

Molecular function

  • proton-transporting ATP synthase activity, rotational mechanism (GO: 0046933)
  • proton-transporting ATPase activity, rotational mechanism (GO: 0046961)

Biological process

#4: Polypeptide(L)ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 15087.244 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: B7MGF1

Cellular component

Molecular function

  • proton-transporting ATP synthase activity, rotational mechanism (GO: 0046933)

Biological process

#5: Polypeptide(L)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: (gene. exp.) Escherichia coli / References: UniProt: P0ABA2

Cellular component

Molecular function

  • proton-transporting ATP synthase activity, rotational mechanism (GO: 0046933)
  • proton-transporting ATPase activity, rotational mechanism (GO: 0046961)

Biological process

#6: Polypeptide(L)ATP synthase subunit a / ATP synthase F0 sector subunit a / F-ATPase subunit 6


Mass: 30324.096 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli / References: UniProt: B7L888

Cellular component

  • integral component of membrane (GO: 0016021)
  • integral component of plasma membrane (GO: 0005887)
  • proton-transporting ATP synthase complex, coupling factor F(o) (GO: 0045263)

Molecular function

  • proton-transporting ATP synthase activity, rotational mechanism (GO: 0046933)

Biological process

  • plasma membrane ATP synthesis coupled proton transport (GO: 0042777)
#7: Polypeptide(L)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: (gene. exp.) Escherichia coli / References: UniProt: B7MGF5

Cellular component

Molecular function

  • proton-transporting ATP synthase activity, rotational mechanism (GO: 0046933)
  • proton-transporting ATPase activity, rotational mechanism (GO: 0046961)

Biological process

#8: Polypeptide(L)
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: (gene. exp.) Escherichia coli / References: UniProt: B7NR39

Cellular component

Molecular function

  • lipid binding (GO: 0008289)
  • proton-transporting ATP synthase activity, rotational mechanism (GO: 0046933)
  • proton-transporting ATPase activity, rotational mechanism (GO: 0046961)

Biological process

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Non-polymers , 2 types, 4 molecules

#9: ChemicalChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP (energy-carrying molecule) *YM


Mass: 507.181 Da / Num. of mol.: 3 / Formula: C10H16N5O13P3
#10: ChemicalChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: ATP synthase / Type: COMPLEX / Entity ID: 1,2,3,4,5,6,7,8,9,10 / Source: RECOMBINANT
Molecular weightValue: 0.558 deg. / Units: MEGADALTONS / Experimental flag: NO
Source (natural)Organism: Escherichia coli
Source (recombinant)Organism: Escherichia coli / Plasmid: pFV2
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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
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: 8.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 95345 / Symmetry type: POINT

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