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- EMDB-1318: Three-dimensional structure of the respiratory chain supercomplex... -

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Basic information

Entry
Database: EMDB / ID: EMD-1318
TitleThree-dimensional structure of the respiratory chain supercomplex I1III2IV1 from bovine heart mitochondria.
Map dataThis is a side view along the mitochondiral membrane plane
Sample
  • Sample: bovine supercomplex I1III2IV1
  • Protein or peptide: complex IRespiratory complex I
  • Protein or peptide: complex IIICoenzyme Q – cytochrome c reductase
  • Protein or peptide: complex IVCytochrome c oxidase
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / negative staining / Resolution: 32.0 Å
AuthorsSchafer E / Dencher NA / Vonck J / Parcej DN
CitationJournal: Biochemistry / Year: 2007
Title: Three-dimensional structure of the respiratory chain supercomplex I1III2IV1 from bovine heart mitochondria.
Authors: Eva Schäfer / Norbert A Dencher / Janet Vonck / David N Parcej /
Abstract: The respiratory chain complexes can arrange into multienzyme assemblies, so-called supercomplexes. We present the first 3D map of a respiratory chain supercomplex. It was determined by random conical ...The respiratory chain complexes can arrange into multienzyme assemblies, so-called supercomplexes. We present the first 3D map of a respiratory chain supercomplex. It was determined by random conical tilt electron microscopy analysis of a bovine supercomplex consisting of complex I, dimeric complex III, and complex IV (I1III2IV1). Within this 3D map the positions and orientations of all the individual complexes in the supercomplex were determined unambiguously. Furthermore, the ubiquinone and cytochrome c binding sites of each complex in the supercomplex could be located. The mobile electron carrier binding site of each complex was found to be in proximity to the binding site of the succeeding complex in the respiratory chain. This provides structural evidence for direct substrate channeling in the supercomplex assembly with short diffusion distances for the mobile electron carriers.
History
DepositionJan 30, 2007-
Header (metadata) releaseFeb 5, 2007-
Map releaseFeb 5, 2008-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.003
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.003
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1318.gif

Downloads & links

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Map

FileDownload / File: emd_1318.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a side view along the mitochondiral membrane plane
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.67 Å/pix.
x 128 pix.
= 597.376 Å		4.67 Å/pix.
x 128 pix.
= 597.376 Å		4.67 Å/pix.
x 128 pix.
= 597.376 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.667 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.003 / Movie #1: 0.003
Minimum - Maximum-0.000237242 - 0.00625119
Average (Standard dev.)0.000906469 (±0.000516844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 597.376 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.6674.6674.667
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z597.376597.376597.376
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-150-149
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0000.0060.001

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Supplemental data

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Sample components

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Entire : bovine supercomplex I1III2IV1

EntireName: bovine supercomplex I1III2IV1
Components
  • Sample: bovine supercomplex I1III2IV1
  • Protein or peptide: complex IRespiratory complex I
  • Protein or peptide: complex IIICoenzyme Q – cytochrome c reductase
  • Protein or peptide: complex IVCytochrome c oxidase

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Supramolecule #1000: bovine supercomplex I1III2IV1

SupramoleculeName: bovine supercomplex I1III2IV1 / type: sample / ID: 1000
Details: membranes are solubilised in digitonin, monodisperse sample
Number unique components: 3
Molecular weightExperimental: 1.7 MDa / Theoretical: 1.7 MDa

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Macromolecule #1: complex I

MacromoleculeName: complex I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / Tissue: heart / Cell: heart / Organelle: mitochondria / Location in cell: inner mitochondrial membrane

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Macromolecule #2: complex III

MacromoleculeName: complex III / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / Tissue: heart / Cell: heart / Organelle: mitochondria / Location in cell: inner mitochondrial membrane

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Macromolecule #3: complex IV

MacromoleculeName: complex IV / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / Tissue: heart / Cell: heart / Organelle: mitochondria / Location in cell: inner mitochondrial membrane

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.1
Details: 0.1 % (w/v) digitonin, 25 mM tricine, 7.5 mM bis-tris, 25 mM aminocaproic acid, 10 % (w/v) glycerol
StainingType: NEGATIVE / Details: 2 % (w/v) ammonium molybdate, deep stain method
GridDetails: 400 mesh Cu grid
VitrificationCryogen name: NONE

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Electron microscopy

MicroscopeFEI/PHILIPS CM120T
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 45000
Sample stageSpecimen holder: n.a / Specimen holder model: OTHER / Tilt angle max: 50
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Number real images: 20
Tilt angle min0

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Image processing

Final two d classificationNumber classes: 3
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: SPIDER / Details: final maps calculated from two / Number images used: 1023
Detailsparticles were selected manually

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Atomic model buiding 1

DetailsThe complexes were fitted by hand in Chimera

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