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

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Basic information

Entry
Database: EMDB / ID: 2091
TitleElectron cryomicroscopy of the bovine mitochondrial ATP synthase
Keywordsbioenergetics / membrane
SampleBovine mitochondrial ATP synthase
SourceBos taurus / mammal / Cow / ウシ /
Map data3D map of bovine ATP synthase
Methodsingle particle reconstruction, at 18 Å resolution
AuthorsBaker LA / Watt IN / Runswick MJ / Walker JE / Rubinstein JL
CitationProc. Natl. Acad. Sci. U.S.A., 2012, 109, 11675-11680

Proc. Natl. Acad. Sci. U.S.A., 2012, 109, 11675-11680 Yorodumi Papers
Arrangement of subunits in intact mammalian mitochondrial ATP synthase determined by cryo-EM.
Lindsay A Baker / Ian N Watt / Michael J Runswick / John E Walker / John L Rubinstein

DateDeposition: Apr 30, 2012 / Header (metadata) release: May 17, 2012 / Map release: Jun 29, 2012 / Last update: Aug 7, 2013

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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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Supplemental images

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Map

Fileemd_2091.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices

Image control

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

Surface

Projections

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level:0.3 (by author), 0.3 (movie #1):
Minimum - Maximum-0.08318548 - 0.80262011
Average (Standard dev.)0.01990009 (0.09413327)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
CellA=B=C: 358.4 Å
α=β=γ: 90 deg.

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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Mask #1

Fileemd_2091_msk.map ( map file in CCP4 format, 8193 KB )
Projections & Slices
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Density Histograms
Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::

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Mask #2

Fileemd_2091_msk_1.map ( map file in CCP4 format, 8193 KB )
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Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::

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Mask #3

Fileemd_2091_msk_2.map ( map file in CCP4 format, 8193 KB )
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Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::

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Mask #4

Fileemd_2091_msk_3.map ( map file in CCP4 format, 8193 KB )
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Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::

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Mask #5

Fileemd_2091_msk_4.map ( map file in CCP4 format, 8193 KB )
Projections & Slices
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Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::

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Mask #6

Fileemd_2091_msk_5.map ( map file in CCP4 format, 8193 KB )
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Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::

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Mask #7

Fileemd_2091_msk_6.map ( map file in CCP4 format, 8193 KB )
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Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::

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Mask #8

Fileemd_2091_msk_7.map ( map file in CCP4 format, 8193 KB )
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Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::

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Mask #9

Fileemd_2091_msk_8.map ( map file in CCP4 format, 8193 KB )
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Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::

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Mask #10

Fileemd_2091_msk_9.map ( map file in CCP4 format, 8193 KB )
Projections & Slices
AxesZYX
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Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::

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Mask #11

Fileemd_2091_msk_10.map ( map file in CCP4 format, 8193 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1
Details::::EMDATABANK.org::::

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Sample components

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Entire Bovine mitochondrial ATP synthase

EntireName: Bovine mitochondrial ATP synthase
Details: The sample was maintained in a buffer containing the detergent dodecylmaltoside and phospholipids
Number of components: 1
Oligomeric State: One hetero oligomeric ATP synthase complex
MassTheoretical: 600 kDa / Experimental: 600 kDa / Measured by: Size exclusion

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Component #1: protein, ATP synthase

ProteinName: ATP synthase / a.k.a: ATPase, complex V / Oligomeric Details: monomer / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 600 kDa / Experimental: 600 kDa
SourceSpecies: Bos taurus / mammal / Cow / ウシ /
Source (natural)Organelle: Mitochondria / Location in cell: Mitochondrial membrane / Organ or tissue: Heart

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 2.5 mg/ml
Buffer solution: 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)
pH: 7.8
Support filmQuantifoil R2/2 grids
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Method: Equilibrate 30 s, blot 10 s

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Jan 1, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: manual astigmatism correction using image FFT / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 3000 - 7000 nm
Specimen HolderHolder: Gatan 626 / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 848 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 57885 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Rotan, Projection matching / Software: Spider, Rotan, Frealign, Build_fspace / CTF correction: Each particle / Resolution: 18 Å / Resolution method: FSC 0.143

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