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- EMDB-8130: Architecture of ovine respiratory supercomplex (I-III2-IV) confor... -

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Entry
Database: EMDB / ID: 8130
TitleArchitecture of ovine respiratory supercomplex (I-III2-IV) conformation tight
Map data
SampleOvine respiratory supercomplex (I-III2-IV), conformation tight
  • (Respiratory complex ...Respiratory system) x 3
Function / homologyCytochrome c oxidase subunit I domain / Di-haem cytochrome, transmembrane / Single alpha-helix domain superfamily / 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 VIIB domain superfamily / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome c1, transmembrane anchor, C-terminal ...Cytochrome c oxidase subunit I domain / Di-haem cytochrome, transmembrane / Single alpha-helix domain superfamily / 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 VIIB domain superfamily / 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 / Rieske [2Fe-2S] iron-sulphur domain / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Insulinase (Peptidase family M16) / Cytochrome b-c1 complex subunit 10 / Rieske iron-sulphur protein / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit IV / Peptidase M16, N-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Metalloenzyme, LuxS/M16 peptidase-like / Globular protein, non-globular alpha/beta subunit / Cytochrome c-like domain / Cupredoxin / Cytochrome C oxidase, subunit VIIB / Cytochrome b / Cytochrome c oxidase subunit III domain / Peptidase M16, C-terminal / Cytochrome b-c1 complex subunit 9 superfamily / 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 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome c oxidase, subunit Vb 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 8 superfamily / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome b-c1 complex subunit 7 superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome c oxidase subunit III-like superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c oxidase subunit III / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome C oxidase subunit II, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit VIc / UcrQ family / Peptidase M16 inactive domain / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome C oxidase chain VIIB / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Rieske iron-sulphur protein, C-terminal / Insulinase family, zinc-binding region signature. / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIa signature. / 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. / Cytochrome oxidase c subunit VIb / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome b/b6, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit 6C / 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 8
Function and homology information
SourceOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / 5.8 Å resolution
AuthorsSazanov LA / Letts JA / Fiedorczuk K
CitationJournal: Nature / Year: 2016
Title: The architecture of respiratory supercomplexes.
Authors: James A Letts / Karol Fiedorczuk / Leonid A Sazanov
Validation ReportPDB-ID: 5j4z

SummaryFull reportAbout validation report
DateDeposition: Mar 19, 2016 / Header (metadata) release: Oct 5, 2016 / Map release: Oct 5, 2016 / Last update: Nov 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5j4z
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8130.map.gz (map file in CCP4 format, 488096 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
496 pix
1.72 Å/pix.
= 853.12 Å
496 pix
1.72 Å/pix.
= 853.12 Å
496 pix
1.72 Å/pix.
= 853.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density
Contour Level:0.12 (by author), 0.12 (movie #1):
Minimum - Maximum-0.21388671 - 0.6936373
Average (Standard dev.)0.000027917682 (0.018666744)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions496496496
Origin0.00.00.0
Limit495.0495.0495.0
Spacing496496496
CellA=B=C: 853.12 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.721.721.72
M x/y/z496496496
origin x/y/z0.0000.0000.000
length x/y/z853.120853.120853.120
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS496496496
D min/max/mean-0.2140.6940.000

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Supplemental data

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Sample components

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Entire Ovine respiratory supercomplex (I-III2-IV), conformation tight

EntireName: Ovine respiratory supercomplex (I-III2-IV), conformation tight
Number of components: 4

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Component #1: protein, Ovine respiratory supercomplex (I-III2-IV), conformation...

ProteinName: Ovine respiratory supercomplex (I-III2-IV), conformation tight
Recombinant expression: No
MassExperimental: 1.71 MDa
SourceSpecies: Ovis aries (sheep)

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Component #2: protein, Respiratory complex IV

ProteinName: Respiratory complex IV / Details: Monomer / Recombinant expression: No
MassTheoretical: 220 kDa
SourceSpecies: Ovis aries (sheep)

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Component #3: protein, Respiratory complex III

ProteinName: Respiratory complex III / Details: Dimer / Recombinant expression: No
MassTheoretical: 490 kDa
SourceSpecies: Ovis aries (sheep)

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Component #4: protein, Respiratory complex I

ProteinName: Respiratory complex I / Details: Monomer / Recombinant expression: No
MassTheoretical: 1000 kDa
SourceSpecies: Ovis aries (sheep)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/ml / pH: 7.7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: Blotted 32 seconds.

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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: 34 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 47000.0 X (nominal), 81395.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 5000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1608 / Sampling size: 14 microns
Details: Images were collected in movie mode with 17 frames per second.

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 18379
3D reconstructionSoftware: RELION / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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