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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: 6719
TitleCryo-EM structure of mammalian respiratory complex I matrix arm
SampleMammalian respiratory complex I matix arm
SourceSus scrofa / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
Map dataThis map was obtained by sub-region refinement with step-by-step reduction of the soft mask.
Methodsingle particle reconstruction, at 3.38 Å resolution
AuthorsGu J / Wu M / Yang M
CitationCell, 2016, 167, 1598-1609.e10

Cell, 2016, 167, 1598-1609.e10 StrPapers
Structure of Mammalian Respiratory Supercomplex I1III2IV1.
Meng Wu / Jinke Gu / Runyu Guo / Yushen Huang / Maojun Yang

DateDeposition: Apr 16, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: Apr 16, 2017

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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
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_6719.map.gz (map file in CCP4 format, 442369 KB)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.08 Å
Density
Contour Level:0.0509 (by author), 0.0509 (movie #1):
Minimum - Maximum-0.22610639 - 0.6859409
Average (Standard dev.)0.0001987006 (0.0050096773)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin000
Limit479479479
Spacing480480480
CellA=B=C: 518.4 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
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 / mammal / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica

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Experimental details

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Sample preparation

Specimen stateparticle
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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