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- EMDB-2011: Structure of the mitochondrial ATP synthase from Saccharomyces ce... -

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Basic information

Entry
Database: EMDB / ID: EMD-2011
TitleStructure of the mitochondrial ATP synthase from Saccharomyces cerevisiae in Brij-35 at 24 Angstroms resolution.
Map dataMap of the Saccharomyces cerevisiae mitochondrial ATP synthase in the detergent Brij-35
Sample
  • Sample: Mitochondrial ATP synthase from Saccharomyces cerevisiae
  • Protein or peptide: ATP synthase
KeywordsATP synthase / membrane protein / cryo-EM / detergent
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 24.0 Å
AuthorsLau WCY / Baker LA / Rubinstein JL
CitationJournal: J Mol Biol / Year: 2008
Title: Cryo-EM structure of the yeast ATP synthase.
Authors: Wilson C Y Lau / Lindsay A Baker / John L Rubinstein /
Abstract: We have used electron cryomicroscopy of single particles to determine the structure of the ATP synthase from Saccharomyces cerevisiae. The resulting map at 24 A resolution can accommodate atomic ...We have used electron cryomicroscopy of single particles to determine the structure of the ATP synthase from Saccharomyces cerevisiae. The resulting map at 24 A resolution can accommodate atomic models of the F(1)-c(10) subcomplex, the peripheral stalk subcomplex, and the N-terminal domain of the oligomycin sensitivity conferral protein. The map is similar to an earlier electron cryomicroscopy structure of bovine mitochondrial ATP synthase but with important differences. It resolves the internal structure of the membrane region of the complex, especially the membrane embedded subunits b, c, and a. Comparison of the yeast ATP synthase map, which lacks density from the dimer-specific subunits e and g, with a map of the bovine enzyme that included e and g indicates where these subunits are located in the intact complex. This new map has allowed construction of a model of subunit arrangement in the F(O) motor of ATP synthase that dictates how dimerization of the complex via subunits e and g might occur.
History
DepositionDec 16, 2011-
Header (metadata) releaseDec 20, 2011-
Map releaseDec 20, 2011-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.18
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2011.png

Downloads & links

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Map

FileDownload / File: emd_2011.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the Saccharomyces cerevisiae mitochondrial ATP synthase in the detergent Brij-35
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.6 Å/pix.
x 64 pix.
= 358.4 Å		5.6 Å/pix.
x 64 pix.
= 358.4 Å		5.6 Å/pix.
x 64 pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.18 / Movie #1: 1.18
Minimum - Maximum-0.56652844 - 3.30214858
Average (Standard dev.)0.07925905 (±0.42508036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.65.65.6
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.5673.3020.079

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Supplemental data

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Sample components

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Entire : Mitochondrial ATP synthase from Saccharomyces cerevisiae

EntireName: Mitochondrial ATP synthase from Saccharomyces cerevisiae
Components
  • Sample: Mitochondrial ATP synthase from Saccharomyces cerevisiae
  • Protein or peptide: ATP synthase

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Supramolecule #1000: Mitochondrial ATP synthase from Saccharomyces cerevisiae

SupramoleculeName: Mitochondrial ATP synthase from Saccharomyces cerevisiae
type: sample / ID: 1000 / Details: Sample contains Brij-35 to maintain solubility / Oligomeric state: One homo-oligomer / Number unique components: 14
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: ATP synthase

MacromoleculeName: ATP synthase / type: protein_or_peptide / ID: 1 / Name.synonym: ATP synthase / Oligomeric state: hetero-oligomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303 / synonym: Baker's yeast / Cell: Saccharomyces cerevisiae / Organelle: Mitochondria / Location in cell: Mitochondrial inner membrane
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 8
Details: 10 mM Tris-HCl, 10 mM NaCl, 2mM MgSO4, 0.05% (v/v) Brij35
GridDetails: 400 mesh Cu/Rh grid with homemade holey carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Details: Vitrification instrument: Vitrobot Mark 3 / Method: Blot from both sides

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Electron microscopy

MicroscopeFEI TECNAI F20
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism corrected around 100,000x magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 103 / Average electron dose: 12 e/Å2 / Od range: 1 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Detailsparticle selected manually
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Rotan, Spider, Frealign / Number images used: 6904

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