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

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Basic information

Entry
Database: EMDB / ID: EMD-4108
TitleCryo-EM of bovine respirasome
Map dataBovine respirasome class 2
Sample
  • Complex: Respirasome
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.4 Å
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 /
Abstract: Respirasomes are macromolecular assemblies of the respiratory chain complexes I, III and IV in the inner mitochondrial membrane. We determined the structure of supercomplex IIIIIV from bovine heart ...Respirasomes are macromolecular assemblies of the respiratory chain complexes I, III and IV in the inner mitochondrial membrane. We determined the structure of supercomplex IIIIIV from bovine heart mitochondria by cryo-EM at 9 Å resolution. Most protein-protein contacts between complex I, III and IV in the membrane are mediated by supernumerary subunits. Of the two Rieske iron-sulfur cluster domains in the complex III dimer, one is resolved, indicating that this domain is immobile and unable to transfer electrons. The central position of the active complex III monomer between complex I and IV in the respirasome is optimal for accepting reduced quinone from complex I over a short diffusion distance of 11 nm, and delivering reduced cytochrome to complex IV. The functional asymmetry of complex III provides strong evidence for directed electron flow from complex I to complex IV through the active complex III monomer in the mammalian supercomplex.
History
DepositionSep 9, 2016-
Header (metadata) releaseSep 21, 2016-
Map releaseNov 16, 2016-
UpdateNov 22, 2017-
Current statusNov 22, 2017Processing site: PDBe / Status: Released

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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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4108.png

Downloads & links

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Map

FileDownload / File: emd_4108.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBovine respirasome class 2
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.082 / Movie #1: 0.082
Minimum - Maximum-0.10275203 - 0.25009614
Average (Standard dev.)0.00093033956 (±0.0157379)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 509.76 Å
α=β=γ: 90.0 °

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
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
Components
  • Complex: Respirasome

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Supramolecule #1: Respirasome

SupramoleculeName: Respirasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#51 / Details: supercomplex of complex I, III and IV
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 1.7 MDa

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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

BufferpH: 7.7
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: 10 s blotting.

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: OTHER / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 2-46 / Number real images: 3592 / Average exposure time: 1.5 sec. / Average electron dose: 70.0 e/Å2 / Details: Falcon III
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 0.0043 µm / Calibrated defocus min: 0.0013 µm / Calibrated magnification: 57797 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 0.0043 µm / Nominal defocus min: 0.0013 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 156519 / Details: particles were selected manually
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: EMDB MAP
EMDB ID:

1876

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 10111
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 7

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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