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- EMDB-8129: Architecture of ovine respiratory supercomplex (I-III2) -

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Basic information

Entry
Database: EMDB / ID: EMD-8129
TitleArchitecture of ovine respiratory supercomplex (I-III2)
Map data
SampleOvine respiratory supercomplex (I-III2)
  • (Respiratory complex ...Respiratory system) x 2
Function / homology
Function and homology information


subthalamus development / pons development / respiratory chain complex III / cerebellar Purkinje cell layer development / pyramidal neuron development / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / thalamus development / ubiquinol-cytochrome-c reductase activity / mitochondrial respiratory chain complex IV ...subthalamus development / pons development / respiratory chain complex III / cerebellar Purkinje cell layer development / pyramidal neuron development / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / thalamus development / ubiquinol-cytochrome-c reductase activity / mitochondrial respiratory chain complex IV / mitochondrial electron transport, ubiquinol to cytochrome c / midbrain development / hypothalamus development / respirasome / hippocampus development / 2 iron, 2 sulfur cluster binding / catalytic activity / metalloendopeptidase activity / mitochondrial inner membrane / nuclear body / electron transfer activity / ubiquitin protein ligase binding / heme binding / mitochondrion / integral component of membrane / nucleoplasm / metal ion binding / cytosol
Rieske iron-sulphur protein, C-terminal / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 10 / Rieske iron-sulphur protein / Peptidase M16, N-terminal / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Cytochrome c1 / Cytochrome b-c1 complex, subunit 6 / Cytochrome c-like domain ...Rieske iron-sulphur protein, C-terminal / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 10 / Rieske iron-sulphur protein / Peptidase M16, N-terminal / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Cytochrome c1 / Cytochrome b-c1 complex, subunit 6 / Cytochrome c-like domain / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b/b6, N-terminal / Cytochrome b/b6, C-terminal / Globular protein, non-globular alpha/beta subunit / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Peptidase M16, C-terminal / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Di-haem cytochrome, transmembrane / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome bc1 complex subunit Rieske, transmembrane domain 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 b-c1 complex subunit 7 superfamily / Cytochrome b / Cytochrome c1, transmembrane anchor, C-terminal / Single alpha-helix domain superfamily / Cytochrome b/b6-like domain superfamily / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 9
Cytochrome b-c1 complex subunit 6 / Cytochrome b / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome c reductase, complex III subunit X / Uncharacterized protein / Ubiquinol-cytochrome c reductase complex III subunit VII / Cytochrome c1 / Ubiquinol-cytochrome c reductase core protein 2 / Ubiquinol-cytochrome c reductase core protein 1
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
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 /
Abstract: Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) ...Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We identify two distinct arrangements of supercomplex CICIIICIV (the respirasome)-a major 'tight' form and a minor 'loose' form (resolved at the resolution of 5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex assembly or disassembly. We have also determined an architecture of supercomplex CICIII at 7.8 Å resolution. All observed density can be attributed to the known 80 subunits of the individual complexes, including 132 transmembrane helices. The individual complexes form tight interactions that vary between the architectures, with complex IV subunit COX7a switching contact from complex III to complex I. The arrangement of active sites within the supercomplex may help control reactive oxygen species production. To our knowledge, these are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain.
Validation ReportPDB-ID: 5j8k

SummaryFull reportAbout validation report
History
DepositionMar 19, 2016-
Header (metadata) releaseOct 5, 2016-
Map releaseOct 5, 2016-
UpdateJul 12, 2017-
Current statusJul 12, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5j8k
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8129.map.gz / Format: CCP4 / Size: 465.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 496 pix.
= 853.12 Å
1.72 Å/pix.
x 496 pix.
= 853.12 Å
1.72 Å/pix.
x 496 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 LevelBy AUTHOR: 0.13 / Movie #1: 0.13
Minimum - Maximum-0.23348482 - 0.48776278
Average (Standard dev.)0.000024742558 (±0.020731922)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions496496496
Spacing496496496
CellA=B=C: 853.12 Å
α=β=γ: 90.0 °

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/NZ00-41
NX/NY/NZ737384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS496496496
D min/max/mean-0.2330.4880.000

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Supplemental data

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Sample components

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Entire Ovine respiratory supercomplex (I-III2)

EntireName: Ovine respiratory supercomplex (I-III2) / Number of components: 3

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

ProteinName: Ovine respiratory supercomplex (I-III2) / Recombinant expression: No
MassTheoretical: 1000 kDa
SourceSpecies: Ovis aries (sheep)

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Component #2: protein, Respiratory complex III

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

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Component #3: protein, Respiratory complex I

ProteinName: Respiratory complex I / Details: Monomer / Recombinant expression: No

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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 µm
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: 9844
3D reconstructionSoftware: RELION / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

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