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- EMDB-0004: Saccharomyces cerevisiae respiratory supercomplex III2IV -

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Entry
Database: EMDB / ID: 0004
TitleSaccharomyces cerevisiae respiratory supercomplex III2IV
Map dataModelling map
SampleSaccharomyces cerevisiae Supercomplex (III2IV)
  • (Saccharomyces cerevisiae complex ...) x 2
  • (Cytochrome b-c1 complex subunit ...) x 8
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • (Cytochrome c oxidase subunit ...) x 9
  • (Cytochrome c oxidase polypeptide ...) x 2
  • Unknown Cox subunit
  • (ligand) x 13
Function / homologyCytochrome c oxidase subunit I domain / Cytochrome b-c1 complex subunit 10, fungi / Cytochrome c oxidase subunit 2, C-terminal / 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 ...Cytochrome c oxidase subunit I domain / Cytochrome b-c1 complex subunit 10, fungi / Cytochrome c oxidase subunit 2, C-terminal / 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 c oxidase, subunit VIa, conserved site / Cytochrome b/b6, C-terminal domain superfamily / Rieske [2Fe-2S] iron-sulphur domain / 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 / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 9 / 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 VIa 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 / Cupredoxin / Peptidase M16, C-terminal / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / 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 / Rieske iron-sulphur protein, C-terminal / 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 oxidase c subunit VIb / Copper centre Cu(A) / Cytochrome c oxidase subunit III-like
Function and homology information
SourceSaccharomyces cerevisiae W303 (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 3.23 Å resolution
AuthorsRathore S / Berndtsson J / Conrad J / Ott M
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Cryo-EM structure of the yeast respiratory supercomplex.
Authors: Sorbhi Rathore / Jens Berndtsson / Lorena Marin-Buera / Julian Conrad / Marta Carroni / Peter Brzezinski / Martin Ott
Validation ReportPDB-ID: 6giq

SummaryFull reportAbout validation report
DateDeposition: May 15, 2018 / Header (metadata) release: Jul 18, 2018 / Map release: Jan 2, 2019 / Last update: Jan 16, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6giq
  • Surface level: 0.33
  • 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_0004.map.gz (map file in CCP4 format, 202613 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
370 pix
1.06 Å/pix.
= 392.2 Å
370 pix
1.06 Å/pix.
= 392.2 Å
370 pix
1.06 Å/pix.
= 392.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.33 (by author), 0.4 (movie #1):
Minimum - Maximum-1.2225217 - 2.422639
Average (Standard dev.)0.008202017 (0.08052676)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions370370370
Origin0.00.00.0
Limit369.0369.0369.0
Spacing370370370
CellA=B=C: 392.19998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z370370370
origin x/y/z0.0000.0000.000
length x/y/z392.200392.200392.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS370370370
D min/max/mean-1.2232.4230.008

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Supplemental data

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Sample components

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Entire Saccharomyces cerevisiae Supercomplex (III2IV)

EntireName: Saccharomyces cerevisiae Supercomplex (III2IV) / Number of components: 38

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Component #1: protein, Saccharomyces cerevisiae Supercomplex (III2IV)

ProteinName: Saccharomyces cerevisiae Supercomplex (III2IV) / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae W303 (yeast)
Source (natural)Organelle: Mitochondria

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Component #2: protein, Saccharomyces cerevisiae complex III

ProteinName: Saccharomyces cerevisiae complex III / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae W303 (yeast)
Source (natural)Organelle: Mitochondria

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Component #3: protein, Saccharomyces cerevisiae complex IV

ProteinName: Saccharomyces cerevisiae complex IV / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae W303 (yeast)
Source (natural)Organelle: Mitochondria

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

ProteinName: Cytochrome b-c1 complex subunit 1, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 50.282594 kDa
SourceSpecies: Baker's yeast (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 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 40.528008 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #6: protein, Cytochrome b

ProteinName: Cytochrome b / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 43.68659 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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

ProteinName: Cytochrome c1, heme protein, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 34.097523 kDa
SourceSpecies: Baker's yeast (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 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.393973 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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

ProteinName: Cytochrome b-c1 complex subunit 6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 17.276074 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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

ProteinName: Cytochrome b-c1 complex subunit 7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.583755 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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

ProteinName: Cytochrome b-c1 complex subunit 8 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 10.987511 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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

ProteinName: Cytochrome b-c1 complex subunit 9 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 7.485334 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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

ProteinName: Cytochrome b-c1 complex subunit 10 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.602913 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #14: protein, Cytochrome c oxidase subunit 1

ProteinName: Cytochrome c oxidase subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.832586 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #15: protein, Cytochrome c oxidase subunit 2

ProteinName: Cytochrome c oxidase subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.585055 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #16: protein, Cytochrome c oxidase subunit 3

ProteinName: Cytochrome c oxidase subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.383582 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #17: protein, Cytochrome c oxidase subunit 4, mitochondrial

ProteinName: Cytochrome c oxidase subunit 4, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.164557 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #18: protein, Cytochrome c oxidase polypeptide 5A, mitochondrial

ProteinName: Cytochrome c oxidase polypeptide 5A, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.161465 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #19: protein, Cytochrome c oxidase subunit 6, mitochondrial

ProteinName: Cytochrome c oxidase subunit 6, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.3666 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #20: protein, Cytochrome c oxidase subunit 7

ProteinName: Cytochrome c oxidase subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.942349 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #21: protein, Cytochrome c oxidase polypeptide VIII, mitochondrial

ProteinName: Cytochrome c oxidase polypeptide VIII, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.921686 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #22: protein, Cytochrome c oxidase subunit 7A

ProteinName: Cytochrome c oxidase subunit 7A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.974226 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #23: protein, Cytochrome c oxidase subunit 6B

ProteinName: Cytochrome c oxidase subunit 6B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.799895 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #24: protein, Cytochrome c oxidase subunit 6A, mitochondrial

ProteinName: Cytochrome c oxidase subunit 6A, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.046146 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #25: protein, Unknown Cox subunit

ProteinName: Unknown Cox subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.656265 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #26: ligand, (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pen...

LigandName: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.592785 kDa

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Component #27: ligand, PROTOPORPHYRIN IX CONTAINING FE

LigandName: PROTOPORPHYRIN IX CONTAINING FE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.616487 kDa

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Component #28: ligand, (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(t...

LigandName: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.691959 kDa

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Component #29: ligand, (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,...

LigandName: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.634631 kDa

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Component #30: ligand, 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-H...

LigandName: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.592891 kDa

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Component #31: ligand, (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetr...

LigandName: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.564732 kDa

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Component #32: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

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Component #33: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.734039 kDa

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Component #34: ligand, (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(...

LigandName: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.593773 kDa

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Component #35: ligand, (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-di...

LigandName: (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.834862 kDa

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Component #36: ligand, COPPER (II) ION

LigandName: COPPER (II) ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.354605 MDa

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Component #37: ligand, HEME-A

LigandName: HEME-A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.852837 kDa

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Component #38: ligand, DINUCLEAR COPPER ION

LigandName: DINUCLEAR COPPER ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.127092 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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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 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 203271
3D reconstructionSoftware: cryoSPARC / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: Cross-Correlation coefficient / Refinement space: REAL
Output model

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