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- EMDB-1357: Structure of the mitochondrial ATP synthase by electron cryomicro... -

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Basic information

Entry
Database: EMDB / ID: EMD-1357
TitleStructure of the mitochondrial ATP synthase by electron cryomicroscopy.
Map data
SampleBovine mitochondrial ATP synthase:
alpha / beta / gamma / delta / epsilon / a / b / c / d / e ...alpha / beta / gamma / delta / epsilon / a / b / c / d / e / f / g / F6 / OSCP / A6L
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 32 Å
AuthorsRubinstein JL / Walker JE / Henderson R
CitationJournal: EMBO J / Year: 2003
Title: Structure of the mitochondrial ATP synthase by electron cryomicroscopy.
Authors: John L Rubinstein / John E Walker / Richard Henderson /
Abstract: We have determined the structure of intact ATP synthase from bovine heart mitochondria by electron cryomicroscopy of single particles. Docking of an atomic model of the F1-c10 subcomplex into a major ...We have determined the structure of intact ATP synthase from bovine heart mitochondria by electron cryomicroscopy of single particles. Docking of an atomic model of the F1-c10 subcomplex into a major segment of the map has allowed the 32 A resolution density to be interpreted as the F1-ATPase, a central and a peripheral stalk and an FO membrane region that is composed of two domains. One domain of FO corresponds to the ring of c-subunits, and the other probably contains the a-subunit, the transmembrane portion of the b-subunit and the remaining integral membrane proteins of FO. The peripheral stalk wraps around the molecule and connects the apex of F1 to the second domain of FO. The interaction of the peripheral stalk with F1-c10 implies that it binds to a non-catalytic alpha-beta interface in F1 and its inclination where it is not attached to F1 suggests that it has a flexible region that can serve as a stator during both ATP synthesis and ATP hydrolysis.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMay 8, 2007-
Header (metadata) releaseMay 9, 2007-
Map releaseMay 9, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.167303869
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.167303869
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1qo1
  • Surface level: 0.167303869
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1357.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 128 pix.
= 358.4 Å
2.8 Å/pix.
x 128 pix.
= 358.4 Å
2.8 Å/pix.
x 128 pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour LevelPrimary: 0.0799 / Movie #1: 0.1673039
Minimum - Maximum-0.14835 - 0.899798
Average (Standard dev.)0.01476 (±0.0974465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 358.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1480.9000.015

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Supplemental data

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Sample components

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Entire Bovine mitochondrial ATP synthase

EntireName: Bovine mitochondrial ATP synthase / Details: Kept in solution with Brij-35 detergent / Oligomeric State: multisubunit complex / Number of components: 15
MassTheoretical: 660 kDa

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Component #1: protein, alpha

ProteinName: alpha / Oligomeric Details: Multiprotein complex / Details: 3 copies / Recombinant expression: No
MassTheoretical: 54.39 kDa / Experimental: 54.39 kDa
SourceSpecies: Bos taurus (cattle)
Source (natural)Organelle: Mitochondrial / Location in cell: Inner mitochondrial membrane / Organ or tissue: Bovine Heart

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Component #2: protein, beta

ProteinName: beta / Details: 3 copies / Recombinant expression: No
MassTheoretical: 51.705 kDa / Experimental: 51.705 kDa
SourceSpecies: Bos taurus (cattle)

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Component #3: protein, gamma

ProteinName: gamma / Recombinant expression: No
MassTheoretical: 30.256 kDa / Experimental: 30.256 kDa
SourceSpecies: Bos taurus (cattle)

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Component #4: protein, delta

ProteinName: delta / Recombinant expression: No
MassTheoretical: 15.065 kDa / Experimental: 15.065 kDa
SourceSpecies: Bos taurus (cattle)

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Component #5: protein, epsilon

ProteinName: epsilon / Recombinant expression: No
MassTheoretical: 5.652 kDa / Experimental: 5.652 kDa
SourceSpecies: Bos taurus (cattle)

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Component #6: protein, a

ProteinName: a / Recombinant expression: No
MassTheoretical: 24.788 kDa / Experimental: 24.788 kDa
SourceSpecies: Bos taurus (cattle)

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Component #7: protein, b

ProteinName: b / Recombinant expression: No
MassTheoretical: 24.669 kDa / Experimental: 24.669 kDa
SourceSpecies: Bos taurus (cattle)

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Component #8: protein, c

ProteinName: c / Details: 9-12 copies / Recombinant expression: No
MassTheoretical: 7.608 kDa / Experimental: 7.608 kDa
SourceSpecies: Bos taurus (cattle)

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Component #9: protein, d

ProteinName: d / Recombinant expression: No
MassTheoretical: 18.561 kDa / Experimental: 18.561 kDa
SourceSpecies: Bos taurus (cattle)

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Component #10: protein, e

ProteinName: e / Recombinant expression: No
MassTheoretical: 8.321 kDa / Experimental: 8.321 kDa
SourceSpecies: Bos taurus (cattle)

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Component #11: protein, f

ProteinName: f / Recombinant expression: No
MassTheoretical: 10.166 kDa / Experimental: 10.166 kDa
SourceSpecies: Bos taurus (cattle)

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Component #12: protein, g

ProteinName: g / Recombinant expression: No
MassTheoretical: 11.286 kDa / Experimental: 11.286 kDa
SourceSpecies: Bos taurus (cattle)

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Component #13: protein, F6

ProteinName: F6 / Recombinant expression: No
MassTheoretical: 8.958 kDa / Experimental: 8.958 kDa
SourceSpecies: Bos taurus (cattle)

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Component #14: protein, OSCP

ProteinName: OSCP / Recombinant expression: No
MassTheoretical: 20.96 kDa / Experimental: 20.96 kDa
SourceSpecies: Bos taurus (cattle)

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Component #15: protein, A6L

ProteinName: A6L / Recombinant expression: No
MassTheoretical: 7.937 kDa / Experimental: 7.937 kDa
SourceSpecies: Bos taurus (cattle)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/mL
Buffer solution: Tris-HCl, 20 mM Sucrose, 50 mM Magnesium Sulfate, 2 mM EDTA, 1 mM ADP, 2 mM Brij-35, 0.05%(w/v)
pH: 8
Support film400 mesh grid coated with a perforated carbon film
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 %
Method: Sample applied from one side and blotted from same side
Details: Vitrification instrument: Talmon plunger. Carried out in coldroom

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Jan 1, 2003 / Details: Digitized with Zeiss SCAI scanner
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Astigmatism: corrected at 175kx magnification / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 3000 - 6000 nm
Specimen HolderHolder: Side entry liquid nitrogen / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 101 / Scanner: ZEISS SCAI / Sampling size: 7 µm / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 5984 / Details: Particles manually selected. / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Rotational Analysis / Software: IMAGIC, FREALIGN, ROTAN / CTF correction: See publication / Resolution: 32 Å / Resolution method: FSC 0.143

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Atomic model buiding

Modeling #1Software: O / Refinement protocol: rigid body
Details: Protocol: Eye. Multiple pdb files fit. See publication.

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