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

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Basic information

Entry
Database: EMDB / ID: EMD-8130
TitleArchitecture of ovine respiratory supercomplex (I-III2-IV) conformation tight
Map dataNone
Sample
  • Complex: Ovine respiratory supercomplex (I-III2-IV), conformation tight
    • Complex: Respiratory complex IV
    • Complex: Respiratory complex III
    • Complex: Respiratory complex I
Function / homology
Function and homology information


respiratory chain complex III / respiratory chain complex IV assembly / respiratory chain complex IV / aerobic electron transport chain / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity ...respiratory chain complex III / respiratory chain complex IV assembly / respiratory chain complex IV / aerobic electron transport chain / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / electron transfer activity / membrane => GO:0016020 / copper ion binding / ubiquitin protein ligase binding / heme binding / proteolysis / nucleoplasm / metal ion binding
Similarity search - Function
Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Ubiquinol-cytochrome c reductase 8kDa, N-terminal ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Cytochrome C oxidase, subunit VIIB domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit VIIa superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome c oxidase subunit VIc / Cytochrome C oxidase chain VIIB / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome b-c1 complex subunit 9 / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome c oxidase subunit III / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Heme-copper oxidase subunit III family profile. / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome c oxidase subunit III-like superfamily / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b / : / : / Cytochrome c/quinol oxidase subunit II / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Rieske iron-sulphur protein, C-terminal / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Cytochrome C oxidase subunit II, periplasmic domain
Similarity search - Domain/homology
Cytochrome b-c1 complex subunit 6 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome b / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome b-c1 complex subunit 7 ...Cytochrome b-c1 complex subunit 6 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome b / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome b-c1 complex subunit 7 / Complex III subunit 9 / Cytochrome c oxidase subunit 8 / Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 4 / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6C / cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial
Similarity search - Component
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 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.
History
DepositionMar 19, 2016-
Header (metadata) releaseOct 5, 2016-
Map releaseOct 5, 2016-
UpdateNov 28, 2018-
Current statusNov 28, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • 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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8130.png

Downloads & links

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Map

FileDownload / File: emd_8130.map.gz / Format: CCP4 / Size: 465.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.12
Minimum - Maximum-0.21388671 - 0.6936373
Average (Standard dev.)0.000027917682 (±0.018666744)
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
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
Components
  • Complex: Ovine respiratory supercomplex (I-III2-IV), conformation tight
    • Complex: Respiratory complex IV
    • Complex: Respiratory complex III
    • Complex: Respiratory complex I

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Supramolecule #1: Ovine respiratory supercomplex (I-III2-IV), conformation tight

SupramoleculeName: Ovine respiratory supercomplex (I-III2-IV), conformation tight
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#68
Source (natural)Organism: Ovis aries (sheep)
Molecular weightExperimental: 1.71 MDa

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Supramolecule #2: Respiratory complex IV

SupramoleculeName: Respiratory complex IV / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#13 / Details: Monomer
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 220 KDa

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Supramolecule #3: Respiratory complex III

SupramoleculeName: Respiratory complex III / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #14-#24 / Details: Dimer
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 490 KDa

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Supramolecule #4: Respiratory complex I

SupramoleculeName: Respiratory complex I / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #25-#68 / Details: Monomer
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 1.0 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 7.7
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloride
20.0 mMHEPES
0.1 %Digitonin
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blotted 32 seconds.
DetailsSingle particles dispersed in digitonin

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 81395 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-32 / Number grids imaged: 3 / Number real images: 1608 / Average exposure time: 4.0 sec. / Average electron dose: 34.0 e/Å2
Details: Images were collected in movie mode with 17 frames per second.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 67650
CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 18379
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-5j4z:
Architecture of tight respirasome

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