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- EMDB-6719: Cryo-EM structure of mammalian respiratory complex I matrix arm -

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Basic information

Entry
Database: EMDB / ID: EMD-6719
TitleCryo-EM structure of mammalian respiratory complex I matrix arm
Map data
SampleMammalian respiratory complex I matix arm
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsGu J / Wu M / Yang M
CitationJournal: Cell / Year: 2016
Title: Structure of Mammalian Respiratory Supercomplex IIIIIV.
Authors: Meng Wu / Jinke Gu / Runyu Guo / Yushen Huang / Maojun Yang /
Abstract: The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to ...The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to synthesize ATP. The precise arrangement of SCs is largely unknown. Here, we report a 4.0-Å cryo-electron microscopy (cryo-EM) structure of the major SC in porcine heart, the 1.7-MDa SCIIIIIV. The complex III (CIII) dimer and complex IV (CIV) bind at the same side of the L-shaped complex I (CI). Several accessory or supernumerary subunits of CI, such as NDUFA11, NDUFB4, NDUFB8, and NDUFB9, directly contribute to the oligomerization of CI, CIII, and CIV. COX7C and COX7A of CIV attach CIV to the concave surface formed by CIII and the distal end of membrane arm of CI. The structure suggests a possible mechanism by which electrons are transferred from NADH to cytochrome c and provides a platform for future functional dissection of respiration.
History
DepositionApr 16, 2017-
Header (metadata) releaseMay 3, 2017-
Map releaseMay 3, 2017-
UpdateMay 3, 2017-
Current statusMay 3, 2017Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0509
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0509
  • 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_6719.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 480 pix.
= 518.4 Å
1.08 Å/pix.
x 480 pix.
= 518.4 Å
1.08 Å/pix.
x 480 pix.
= 518.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.0509 / Movie #1: 0.0509
Minimum - Maximum-0.22610639 - 0.6859409
Average (Standard dev.)0.0001987006 (±0.0050096773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 518.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z518.400518.400518.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.2260.6860.000

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Supplemental data

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Sample components

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Entire Mammalian respiratory complex I matix arm

EntireName: Mammalian respiratory complex I matix arm / Details: Respiratory complex I matix arm from Sus scrofa / Number of components: 1

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Component #1: protein, Mammalian respiratory complex I matix arm

ProteinName: Mammalian respiratory complex I matix arm / Details: Respiratory complex I matix arm from Sus scrofa / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL / pH: 7.4
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: 1.25 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 161912
3D reconstructionSoftware: RELION / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF

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