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- EMDB-5319: Three-dimensional structure of bovine respirasome by single parti... -

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Basic information

Entry
Database: EMDB / ID: 5319
TitleThree-dimensional structure of bovine respirasome by single particle cryo-electron tomography
Map dataEM map of respirasome from bovine mitochondria
SampleRespirasome from bovine mitochondria:
respirasome
KeywordsOxidative phosphorylation / mitochondria
SourceBos taurus (cattle)
Methodsubtomogram averaging / cryo EM / negative staining / 22 Å resolution
AuthorsDudkina NV / Kudryashev M / Stahlberg H / Boekema EJ
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2011
Title: Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography.
Authors: Natalya V Dudkina / Mikhail Kudryashev / Henning Stahlberg / Egbert J Boekema
DateDeposition: Jul 5, 2011 / Header (metadata) release: Jul 13, 2011 / Map release: Aug 31, 2011 / Last update: Sep 7, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5319.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
3.8 Å/pix.
= 486.4 Å
128 pix
3.8 Å/pix.
= 486.4 Å
128 pix
3.8 Å/pix.
= 486.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.8 Å
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.230164 - 0.38968
Average (Standard dev.)0.000151277 (0.0353204)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
CellA=B=C: 486.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.83.83.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z486.400486.400486.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.2300.3900.000

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Supplemental data

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Sample components

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Entire Respirasome from bovine mitochondria

EntireName: Respirasome from bovine mitochondria
Details: The sample was thawed from storage at -80 degrees Celcius before being loaded onto the grid.
Number of components: 1
Oligomeric State: One monomer of NADH dehydrogenase binds to one dimer of cytochrome bc1 and one monomer of cytochrome c oxidase
MassTheoretical: 1.7 MDa / Experimental: 1.7 MDa / Measured by: blue-native gel electrophoresis

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Component #1: protein, respirasome

ProteinName: respirasome / a.k.a: respirasome / Oligomeric Details: monomer / Details: Solubilized with digitonin / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 1.7 MDa / Experimental: 1.7 MDa
SourceSpecies: Bos taurus (cattle) / Strain: wild type
Source (natural)Organelle: mitochondrion / Location in cell: inner mitochondrial membrane / Cell: heart muscle cells / Organ or tissue: heart

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining, cryo EM
Sample solutionSpecimen conc.: 0.5 mg/ml
Buffer solution: 25 mM Tricine, 7.5 mM Bis-Tris, 0.1 mM PMSF, 0.01% digitonin
pH: 7
Support film200 mesh copper Quantifoil grids with an additional carbon support film
Staining2.5 microliters were mixed with 10-nm gold particles as fiducial markers and applied on glow-discharged 200 mesh Quantifoil support grids with an additional carbon support film. Grids were blotted at 100% humidity for 4-6 seconds at a blot offset (the longitudinal grid positioning) setting of -3.5, using a Vitrobot Mk3 (FEI).
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 89 K / Humidity: 100 % / Method: Blot for 4-6 seconds before plunging / Details: Vitrification instrument: Vitrobot Mk3 (FEI)

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Date: Mar 1, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 80 e/Å2 / Electron beam tilt params: 0 / Illumination mode: SPOT SCAN
LensMagnification: 34000 X (nominal)
Astigmatism: objective lens astigmatism was corrected at 34,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 nm / Energy filter: FEI / Energy window: 0-20 eV
Specimen HolderHolder: Multispecimen holder / Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: -70 - 70 deg. / Temperature: 77 K ( 15 - K)
CameraDetector: GENERIC GATAN (2k x 2k)

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Image acquisition

Image acquisitionNumber of digital images: 21 / Sampling size: 0.38 microns

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Image processing

ProcessingMethod: subtomogram averaging
Details: The particles were selected from the tomograms by cross-correlation to an artificial globular reference followed by manual selection of particle volumes. Average number of projections used in the 3D reconstructions: 2466. Average number of class averages: 1.
3D reconstructionAlgorithm: 60 sections of 6 nm thickness / Software: IMOD, XMIPP, AV3 / Resolution: 22 Å / Resolution method: the 0.5 information threshold criterion

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Atomic model buiding

Modeling #1Software: UCSF Chimera / Refinement protocol: rigid body / Target criteria: cross correlation / Refinement space: REAL / Details: Protocol: Rigid Body
Input PDB model: 1BGY
Modeling #2Software: UCSF Chimera / Refinement protocol: rigid body / Target criteria: cross correlation / Refinement space: REAL / Details: Protocol: Rigid Body
Input PDB model: 1OCC
Modeling #3Software: UCSF Chimera / Refinement protocol: rigid body / Target criteria: cross correlation / Refinement space: REAL / Details: Protocol: Rigid Body
Input PDB model: 3M9S

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