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- EMDB-2091: Electron cryomicroscopy of the bovine mitochondrial ATP synthase -

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Basic information

Entry
Database: EMDB / ID: EMD-2091
TitleElectron cryomicroscopy of the bovine mitochondrial ATP synthase
Map data3D map of bovine ATP synthase
Sample
  • Sample: Bovine mitochondrial ATP synthase
  • Protein or peptide: ATP synthase
Keywordsbioenergetics / membrane
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.0 Å
AuthorsBaker LA / Watt IN / Runswick MJ / Walker JE / Rubinstein JL
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Arrangement of subunits in intact mammalian mitochondrial ATP synthase determined by cryo-EM.
Authors: Lindsay A Baker / Ian N Watt / Michael J Runswick / John E Walker / John L Rubinstein /
Abstract: Mitochondrial ATP synthase is responsible for the synthesis of ATP, a universal energy currency in cells. Whereas X-ray crystallography has revealed the structure of the soluble region of the complex ...Mitochondrial ATP synthase is responsible for the synthesis of ATP, a universal energy currency in cells. Whereas X-ray crystallography has revealed the structure of the soluble region of the complex and the membrane-intrinsic c-subunits, little is known about the structure of the six other proteins (a, b, f, A6L, e, and g) that comprise the membrane-bound region of the complex in animal mitochondria. Here, we present the structure of intact bovine mitochondrial ATP synthase at ∼18 Å resolution by electron cryomicroscopy of single particles in amorphous ice. The map reveals that the a-subunit and c(8)-ring of the complex interact with a small contact area and that the b-subunit spans the membrane without contacting the c(8)-ring. The e- and g-subunits extend from the a-subunit density distal to the c(8)-ring. The map was calculated from images of a preparation of the enzyme solubilized with the detergent dodecyl maltoside, which is visible in electron cryomicroscopy maps. The structure shows that the micelle surrounding the complex is curved. The observed bend in the micelle of the detergent-solubilized complex is consistent with previous electron tomography experiments and suggests that monomers of ATP synthase are sufficient to produce curvature in lipid bilayers.
History
DepositionApr 30, 2012-
Header (metadata) releaseMay 17, 2012-
Map releaseJun 29, 2012-
UpdateAug 7, 2013-
Current statusAug 7, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2091.png

Downloads & links

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Map

FileDownload / File: emd_2091.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of bovine ATP synthase
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

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Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.08318548 - 0.80262011
Average (Standard dev.)0.01990009 (±0.09413327)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

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/NZ000
NX/NY/NZ128128168
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0830.8030.020

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Supplemental data

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Segmentation: #2

Fileemd_2091_msk_1.map
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Fileemd_2091_msk_10.map
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Fileemd_2091_msk_2.map
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Fileemd_2091_msk_3.map
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Fileemd_2091_msk_4.map
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Fileemd_2091_msk_5.map
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Fileemd_2091_msk_6.map
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Fileemd_2091_msk_7.map
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Fileemd_2091_msk_8.map
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Sample components

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Entire : Bovine mitochondrial ATP synthase

EntireName: Bovine mitochondrial ATP synthase
Components
  • Sample: Bovine mitochondrial ATP synthase
  • Protein or peptide: ATP synthase

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Supramolecule #1000: Bovine mitochondrial ATP synthase

SupramoleculeName: Bovine mitochondrial ATP synthase / type: sample / ID: 1000
Details: The sample was maintained in a buffer containing the detergent dodecylmaltoside and phospholipids
Oligomeric state: One hetero oligomeric ATP synthase complex
Number unique components: 1
Molecular weightExperimental: 600 KDa / Theoretical: 600 KDa / Method: Size exclusion

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Macromolecule #1: ATP synthase

MacromoleculeName: ATP synthase / type: protein_or_peptide / ID: 1 / Name.synonym: ATPase, complex V / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: Cow / Tissue: Heart / Organelle: Mitochondria / Location in cell: Mitochondrial membrane
Molecular weightExperimental: 600 KDa / Theoretical: 600 KDa

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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

Concentration2.5 mg/mL
BufferpH: 7.8
Details: 20 mM Tris-HCl, 100 mM NaCl, 2 mM MgSO4, 1 mM ATP, 0.02%[w/v] sodium azide, 0.1 % dodecylmaltoside, 0.1 mg/ml lipids (cardiolipin:PE:PC 3:1:1)
GridDetails: Quantifoil R2/2 grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Method: Equilibrate 30 s, blot 10 s

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Electron microscopy

MicroscopeFEI TECNAI F20
Alignment procedureLegacy - Astigmatism: manual astigmatism correction using image FFT
DateJan 1, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 848 / Average electron dose: 25 e/Å2 / 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: 7.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Spider, Rotan, Frealign, Build_fspace / Number images used: 57885

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