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- EMDB-0268: Complex IV in the III2-IV2 mitochondrial respiratory supercomplex... -

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Basic information

Entry
Database: EMDB / ID: 0268
TitleComplex IV in the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae (CIVb)
Map dataThe second complex IV of the III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae
Sample12-subunit cytochrome c oxidase with isoform Cox5A:
Cox1 / Cox2Cytochrome c oxidase subunit II / Cox3 / Cox4 / Cox5A / Cox6 / Cox7 / Cox8 / Cox9 / Cox12 ...Cox1 / Cox2Cytochrome c oxidase subunit II / Cox3 / Cox4 / Cox5A / Cox6 / Cox7 / Cox8 / Cox9 / Cox12 / Cox13 / Cox26
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 3.38 Å resolution
AuthorsHartley AM / Lukoyanova N / Pinotsis N / Marechal A
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc.
Authors: Andrew M Hartley / Natalya Lukoyanova / Yunyi Zhang / Alfredo Cabrera-Orefice / Susanne Arnold / Brigitte Meunier / Nikos Pinotsis / Amandine Maréchal
DateDeposition: Oct 3, 2018 / Header (metadata) release: Oct 10, 2018 / Map release: Dec 26, 2018 / Last update: Dec 26, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0268.map.gz (map file in CCP4 format, 119165 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
310 pix
1.39 Å/pix.
= 429.691 Å
310 pix
1.39 Å/pix.
= 429.691 Å
310 pix
1.39 Å/pix.
= 429.691 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3861 Å
Density
Contour Level:0.011 (by author), 0.03 (movie #1):
Minimum - Maximum-0.1074029 - 0.19403128
Average (Standard dev.)0.00014159399 (0.004339733)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions310310310
Origin0.00.00.0
Limit309.0309.0309.0
Spacing310310310
CellA=B=C: 429.691 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.38611.38611.3861
M x/y/z310310310
origin x/y/z0.0000.0000.000
length x/y/z429.691429.691429.691
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS310310310
D min/max/mean-0.1070.1940.000

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Supplemental data

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Sample components

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Entire 12-subunit cytochrome c oxidase with isoform Cox5A

EntireName: 12-subunit cytochrome c oxidase with isoform Cox5A / Number of components: 13

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Component #1: protein, 12-subunit cytochrome c oxidase with isoform Cox5A

ProteinName: 12-subunit cytochrome c oxidase with isoform Cox5A / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: W303-1B

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Component #2: protein, Cox1

ProteinName: Cox1 / Recombinant expression: No

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Component #3: protein, Cox2

ProteinName: Cox2Cytochrome c oxidase subunit II / Recombinant expression: No

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Component #4: protein, Cox3

ProteinName: Cox3 / Recombinant expression: No

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Component #5: protein, Cox4

ProteinName: Cox4 / Recombinant expression: No

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Component #6: protein, Cox5A

ProteinName: Cox5A / Recombinant expression: No

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Component #7: protein, Cox6

ProteinName: Cox6 / Recombinant expression: No

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Component #8: protein, Cox7

ProteinName: Cox7 / Recombinant expression: No

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Component #9: protein, Cox8

ProteinName: Cox8 / Recombinant expression: No

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Component #10: protein, Cox9

ProteinName: Cox9 / Recombinant expression: No

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Component #11: protein, Cox12

ProteinName: Cox12 / Recombinant expression: No

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Component #12: protein, Cox13

ProteinName: Cox13 / Recombinant expression: No

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Component #13: protein, Cox26

ProteinName: Cox26 / Recombinant expression: No

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 92 %
Details: 3 uL of sample applied to negatively glow discharged grid, blot force -10; blotting time 8.5 sec.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.645 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 44915
3D reconstructionSoftware: RELION / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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