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- EMDB-11368: bovine ATP synthase monomer state 2 (combined) -

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Basic information

Entry
Database: EMDB / ID: EMD-11368
Titlebovine ATP synthase monomer state 2 (combined)
Map data
SampleBovine ATP synthase
  • monomeric bovine ATP synthase, state 2
  • (ATP synthase ...) x 16
  • ATPase inhibitor, mitochondrial
  • ATP synthase-coupling factor 6, mitochondrial
  • (ligand) x 6
Function / homology
Function and homology information


angiostatin binding / proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex assembly / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial envelope / mitochondrial proton-transporting ATP synthase complex / mitochondrial ATP synthesis coupled proton transport / ATP biosynthetic process ...angiostatin binding / proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex assembly / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial envelope / mitochondrial proton-transporting ATP synthase complex / mitochondrial ATP synthesis coupled proton transport / ATP biosynthetic process / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / negative regulation of endothelial cell proliferation / proton transmembrane transport / negative regulation of ATPase activity / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase complex, catalytic core F(1) / ATP synthesis coupled proton transport / proton transmembrane transporter activity / heme biosynthetic process / H+-transporting two-sector ATPase / aerobic respiration / negative regulation of hydrolase activity / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / erythrocyte differentiation / ADP binding / mitochondrial inner membrane / protein homotetramerization / ATPase binding / calmodulin binding / lipid binding / ATPase / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / integral component of membrane / ATP binding / identical protein binding / plasma membrane
ATP synthase, F1 complex, beta subunit / AAA+ ATPase domain / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATP synthase, F0 complex, subunit A, active site / ATPase, OSCP/delta subunit, conserved site / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit A ...ATP synthase, F1 complex, beta subunit / AAA+ ATPase domain / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATP synthase, F0 complex, subunit A, active site / ATPase, OSCP/delta subunit, conserved site / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit A / ATPase, OSCP/delta subunit / ATP synthase, alpha subunit, C-terminal / ATP synthase protein 8, metazoa / ATP synthase, F1 complex, delta/epsilon subunit / V-ATPase proteolipid subunit C-like domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F0 complex, subunit G, mitochondrial / Mitochondrial ATPase inhibitor / ATP synthase, F0 complex, subunit E, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase membrane subunit K / ATP synthase subunit ATP5MJ, mitochondrial / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase subunit g, animal / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase, F1 complex, gamma subunit conserved site / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F1 complex, gamma subunit superfamily / F/V-ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit A superfamily / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, alpha subunit, C-terminal domain superfamily / F1F0 ATP synthase subunit C superfamily / P-loop containing nucleoside triphosphate hydrolase / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase protein 8, mammals / ATP synthase-coupling factor 6 superfamily, mitochondrial
ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit g, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit e, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase F(0) complex subunit C2, mitochondrial ...ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit g, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit e, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit ATP5MJ, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase protein 8 / ATPase inhibitor, mitochondrial / ATP synthase subunit a / ATP synthase subunit beta, mitochondrial / ATP synthase membrane subunit K, mitochondrial
Biological speciesBos taurus (cattle) / Bovine (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsSpikes TE / Montgomery MG / Walker JE
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009858/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105663150 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of the dimeric ATP synthase from bovine mitochondria.
Authors: Tobias E Spikes / Martin G Montgomery / John E Walker /
Abstract: The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial ...The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. It also describes wedge structures in the membrane domains of each monomer, where the skeleton of each wedge is provided by three α-helices in the membrane domains of the b-subunit to which the supernumerary subunits e, f, and g and the membrane domain of subunit A6L are bound. Protein voids in the wedge are filled by three specifically bound cardiolipin molecules and two other phospholipids. The external surfaces of the wedges link the monomeric complexes together into the dimeric structures and provide a pivot to allow the monomer-monomer interfaces to change during catalysis and to accommodate other changes not related directly to catalysis in the monomer-monomer interface that occur in mitochondrial cristae. The structure of the bovine dimer also demonstrates that the structures of dimeric ATP synthases in a tetrameric porcine enzyme have been seriously misinterpreted in the membrane domains.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 10, 2020-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 8.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zqm
  • Surface level: 8.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11368.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 500 pix.
= 524. Å
1.05 Å/pix.
x 500 pix.
= 524. Å
1.05 Å/pix.
x 500 pix.
= 524. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density
Contour LevelBy AUTHOR: 8.4 / Movie #1: 8.4
Minimum - Maximum-26.711363 - 52.28754
Average (Standard dev.)0.015261618 (±1.0967349)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 524.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z524.000524.000524.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ500500500
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-26.71152.2880.015

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Supplemental data

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Sample components

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Entire Bovine ATP synthase

EntireName: Bovine ATP synthase / Details: bovine ATP synthase inhibited by IF1 1-60His / Number of components: 27

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Component #1: protein, Bovine ATP synthase

ProteinName: Bovine ATP synthase / Details: bovine ATP synthase inhibited by IF1 1-60His / Recombinant expression: No
MassExperimental: 7.441 kDa

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Component #2: protein, monomeric bovine ATP synthase, state 2

ProteinName: monomeric bovine ATP synthase, state 2
Details: monomeric bovine ATP synthase inhibited by IF1 1-60His, state 2
Recombinant expression: No
SourceSpecies: Bos taurus (cattle)

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Component #3: protein, Bovine ATP synthase

ProteinName: Bovine ATP synthase / Recombinant expression: No
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, ATP synthase subunit alpha, mitochondrial

ProteinName: ATP synthase subunit alpha, mitochondrial / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 55.302191 kDa
SourceSpecies: Bovine (cattle)

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Component #5: protein, ATP synthase subunit beta, mitochondrial

ProteinName: ATP synthase subunit beta, mitochondrial / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 51.757836 kDa
SourceSpecies: Bovine (cattle)

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Component #6: protein, ATP synthase subunit gamma, mitochondrial

ProteinName: ATP synthase subunit gamma, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.30076 kDa
SourceSpecies: Bovine (cattle)

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Component #7: protein, ATP synthase subunit delta, mitochondrial

ProteinName: ATP synthase subunit delta, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.074813 kDa
SourceSpecies: Bovine (cattle)

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Component #8: protein, ATP synthase subunit epsilon, mitochondrial

ProteinName: ATP synthase subunit epsilon, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.662693 kDa
SourceSpecies: Bovine (cattle)

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Component #9: protein, ATPase inhibitor, mitochondrial

ProteinName: ATPase inhibitor, mitochondrial
Details: ATP synthase inhibitor protein IF1 residues 1-60 with a 6His tag
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.462098 kDa
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #10: protein, ATP synthase F(0) complex subunit C2, mitochondrial

ProteinName: ATP synthase F(0) complex subunit C2, mitochondrial
Details: Residue 43 is trimethyl-lysine. A postranslational modification.
Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 7.653034 kDa
SourceSpecies: Bovine (cattle)

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Component #11: protein, ATP synthase subunit O, mitochondrial

ProteinName: ATP synthase subunit O, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.959777 kDa
SourceSpecies: Bovine (cattle)

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Component #12: protein, ATP synthase protein 8

ProteinName: ATP synthase protein 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.944523 kDa
SourceSpecies: Bovine (cattle)

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Component #13: protein, ATP synthase subunit a

ProteinName: ATP synthase subunit a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.801785 kDa
SourceSpecies: Bovine (cattle)

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Component #14: protein, ATP synthase subunit d, mitochondrial

ProteinName: ATP synthase subunit d, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.588256 kDa
SourceSpecies: Bovine (cattle)

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Component #15: protein, ATP synthase subunit f, mitochondrial

ProteinName: ATP synthase subunit f, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.184011 kDa
SourceSpecies: Bovine (cattle)

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Component #16: protein, ATP synthase subunit g, mitochondrial

ProteinName: ATP synthase subunit g, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.298196 kDa
SourceSpecies: Bovine (cattle)

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Component #17: protein, ATP synthase subunit ATP5MPL, mitochondrial

ProteinName: ATP synthase subunit ATP5MPL, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.846093 kDa
SourceSpecies: Bovine (cattle)

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Component #18: protein, ATP synthase F(0) complex subunit B1, mitochondrial

ProteinName: ATP synthase F(0) complex subunit B1, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.702709 kDa
SourceSpecies: Bovine (cattle)

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Component #19: protein, ATP synthase-coupling factor 6, mitochondrial

ProteinName: ATP synthase-coupling factor 6, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.971079 kDa
SourceSpecies: Bovine (cattle)

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Component #20: protein, ATP synthase membrane subunit DAPIT, mitochondrial

ProteinName: ATP synthase membrane subunit DAPIT, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.312383 kDa
SourceSpecies: Bovine (cattle)

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Component #21: protein, ATP synthase subunit e, mitochondrial

ProteinName: ATP synthase subunit e, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.205492 kDa
SourceSpecies: Bovine (cattle)

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Component #22: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #23: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #24: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #25: ligand, CARDIOLIPIN

LigandName: CARDIOLIPIN / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 1.464043 kDa

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Component #26: ligand, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

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Component #27: ligand, water

LigandName: water / Number of Copies: 17 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 4.5 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 294 K / Humidity: 100 %
Details: The sample was allowed to penetrate through the holey support and to distribute to both sides of the grid surface for ca. 15 sec. Then the grids were blotted with filter paper for 8-10 sec before blotting..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4.6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 90850
3D reconstructionSoftware: RELION / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 2V7Q, 2V7Q, 2V7Q, 2V7Q, 2V7Q, 2V7Q, 2V7Q, 2V7Q, 2V7Q, 2V7Q, 2CLY, 2CLY, 2CLY
Chain ID: A, B, C, D, E, F, G, H, I, J, A, B, C
Output model

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