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- EMDB-0262: III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae -

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Basic information

Entry
Database: EMDB / ID: 0262
TitleIII2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae
Map dataThe sharpened map of the III2IV2 supercomplex
SampleIII2-IV2 mitochondrial respiratory supercomplex
  • 10-subunit yeast cytochrome bc1
  • 12-subunit cytochrome c oxidase with isoform Cox5A
  • (Cytochrome b-c1 complex subunit ...) x 8
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • Cox1
  • Cox2Cytochrome c oxidase subunit II
  • Cox3
  • Cox4
  • Cox5A
  • Cox6
  • Cox7
  • Cox8
  • Cox9
  • Cox12
  • Cox13
  • Cox26
Function / homologyCytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Va / Cytochrome b / Cytochrome b/b6-like domain superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Ubiquinol-cytochrome C reductase hinge domain ...Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Va / Cytochrome b / Cytochrome b/b6-like domain superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c oxidase, subunit Vb, zinc binding site / Cytochrome b-c1 complex subunit 10, fungi / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome c oxidase subunit III-like superfamily / Di-haem cytochrome, transmembrane / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome c oxidase subunit VII, budding yeast / Rieske iron-sulphur protein / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit III, 4-helical bundle / Peptidase M16, N-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cupredoxin / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome b/b6, C-terminal domain superfamily / Peptidase M16, C-terminal / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome C1 family / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Vb / Insulinase (Peptidase family M16) / Cytochrome c oxidase subunit III / Rieske [2Fe-2S] domain / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6/petB / Cytochrome b(C-terminal)/b6/petD / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase-like, subunit I superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c-like domain superfamily / Ubiquinol-cytochrome C reductase hinge domain superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome b-c1 complex subunit 7 superfamily / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Rieske iron-sulphur protein, C-terminal / Cytochrome c oxidase subunit IV / UcrQ family / Peptidase M16 inactive domain / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Heme-copper oxidase catalytic subunit, copper B binding region signature. / CO II and nitrous oxide reductase dinuclear copper centers signature. / Insulinase family, zinc-binding region signature. / Cytochrome c oxidase subunit VIa signature. / Cytochrome C oxidase subunit II, transmembrane domain / Heme-copper oxidase subunit III family profile. / Cytochrome oxidase subunit I profile. / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b/b6 N-terminal region profile. / Cytochrome b/b6 C-terminal region profile. / Cytochrome c family profile. / Rieske [2Fe-2S] iron-sulfur domain profile. / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Ubiquinol cytochrome reductase transmembrane region / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit VII / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome b/b6, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome b-c1 complex subunit 7 / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome c1 / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III-like / Cytochrome oxidase c subunit VIb / Peptidase M16, zinc-binding site
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 3.31 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
Validation ReportPDB-ID: 6hu9

SummaryFull reportAbout validation report
DateDeposition: Sep 27, 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: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6hu9
  • Surface level: 0.0263
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0262.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:0.0263 (by author), 0.035 (movie #1):
Minimum - Maximum-0.14692926 - 0.2550798
Average (Standard dev.)0.0005225369 (0.009231779)
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-0.1470.2550.001

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Supplemental data

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Sample components

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Entire III2-IV2 mitochondrial respiratory supercomplex

EntireName: III2-IV2 mitochondrial respiratory supercomplex / Number of components: 25

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Component #1: protein, III2-IV2 mitochondrial respiratory supercomplex

ProteinName: III2-IV2 mitochondrial respiratory supercomplex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: W303-1B

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Component #2: protein, 10-subunit yeast cytochrome bc1

ProteinName: 10-subunit yeast cytochrome bc1 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: W303-1B

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Component #3: protein, 12-subunit cytochrome c oxidase with isoform Cox5A

ProteinName: 12-subunit cytochrome c oxidase with isoform Cox5A / Recombinant expression: No

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Component #4: protein, Cytochrome b-c1 complex subunit 1, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 1, mitochondrial / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #5: protein, Cytochrome b-c1 complex subunit 2, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit 2, mitochondrial / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #6: protein, Cytochrome b

ProteinName: Cytochrome b / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #7: protein, Cytochrome c1, heme protein, mitochondrial

ProteinName: Cytochrome c1, heme protein, mitochondrial / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #8: protein, Cytochrome b-c1 complex subunit Rieske, mitochondrial

ProteinName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #9: protein, Cytochrome b-c1 complex subunit 6

ProteinName: Cytochrome b-c1 complex subunit 6 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #10: protein, Cytochrome b-c1 complex subunit 7

ProteinName: Cytochrome b-c1 complex subunit 7 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #11: protein, Cytochrome b-c1 complex subunit 8

ProteinName: Cytochrome b-c1 complex subunit 8 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #12: protein, Cytochrome b-c1 complex subunit 9

ProteinName: Cytochrome b-c1 complex subunit 9 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #13: protein, Cytochrome b-c1 complex subunit 10

ProteinName: Cytochrome b-c1 complex subunit 10 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #14: protein, Cox1

ProteinName: Cox1 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #15: protein, Cox2

ProteinName: Cox2Cytochrome c oxidase subunit II / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #16: protein, Cox3

ProteinName: Cox3 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #17: protein, Cox4

ProteinName: Cox4 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #18: protein, Cox5A

ProteinName: Cox5A / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #19: protein, Cox6

ProteinName: Cox6 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #20: protein, Cox7

ProteinName: Cox7 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #21: protein, Cox8

ProteinName: Cox8 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #22: protein, Cox9

ProteinName: Cox9 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #23: protein, Cox12

ProteinName: Cox12 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #24: protein, Cox13

ProteinName: Cox13 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #25: protein, Cox26

ProteinName: Cox26 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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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: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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