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- EMDB-4108: Cryo-EM of bovine respirasome -

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Basic information

Entry
Database: EMDB / ID: 4108
TitleCryo-EM of bovine respirasome
Map dataBovine respirasome class 2
SampleRespirasome:
SourceBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / 10.4 Å resolution
AuthorsSousa JS / Mills DJ / Vonck J / Kuehlbrandt W
CitationJournal: Elife / Year: 2016
Title: Functional asymmetry and electron flow in the bovine respirasome.
Authors: Joana S Sousa / Deryck J Mills / Janet Vonck / Werner Kühlbrandt
DateDeposition: Sep 9, 2016 / Header (metadata) release: Sep 21, 2016 / Map release: Nov 16, 2016 / Last update: Nov 22, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.082
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.082
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4108.map.gz (map file in CCP4 format, 95552 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
1.77 Å/pix.
= 509.76 Å
288 pix
1.77 Å/pix.
= 509.76 Å
288 pix
1.77 Å/pix.
= 509.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density
Contour Level:0.082 (by author), 0.082 (movie #1):
Minimum - Maximum-0.10275203 - 0.25009614
Average (Standard dev.)0.00093033956 (0.0157379)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin0.00.00.0
Limit287.0287.0287.0
Spacing288288288
CellA=B=C: 509.76 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z509.760509.760509.760
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.1030.2500.001

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Supplemental data

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Sample components

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Entire Respirasome

EntireName: Respirasome / Details: supercomplex of complex I, III and IV / Number of components: 1

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Component #1: protein, Respirasome

ProteinName: Respirasome / Details: supercomplex of complex I, III and IV / Recombinant expression: No
MassTheoretical: 1.7 MDa
SourceSpecies: Bos taurus (cattle)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 90 % / Details: 10 s blotting.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 7 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal), 57797.0 X (calibrated) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1.3 - 4.3 nm
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of digital images: 3592 / Sampling size: 14 microns / Details: Falcon III

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 10111
3D reconstructionSoftware: RELION / Resolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL

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