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- EMDB-4090: Ovine respiratory complex I, peripheral arm -

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Basic information

Entry
Database: EMDB / ID: 4090
TitleOvine respiratory complex I, peripheral arm
Map data
SampleComplex IRespiratory complex I:
SourceOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsFiedorczuk K / Letts JA / Sazanov LA
CitationJournal: Nature / Year: 2016
Title: Atomic structure of the entire mammalian mitochondrial complex I.
Authors: Karol Fiedorczuk / James A Letts / Gianluca Degliesposti / Karol Kaszuba / Mark Skehel / Leonid A Sazanov
DateDeposition: Aug 3, 2016 / Header (metadata) release: Aug 24, 2016 / Map release: Oct 19, 2016 / Last update: Nov 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.144
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.144
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4090.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.39 Å/pix.
= 711.68 Å
512 pix
1.39 Å/pix.
= 711.68 Å
512 pix
1.39 Å/pix.
= 711.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour Level:0.144 (by emdb), 0.144 (movie #1):
Minimum - Maximum-0.43860564 - 1.466241
Average (Standard dev.)-0.00027579855 (0.017859584)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin0.00.00.0
Limit511.0511.0511.0
Spacing512512512
CellA=B=C: 711.68 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z711.680711.680711.680
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.4391.466-0.000

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Supplemental data

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Sample components

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Entire Complex I

EntireName: Complex I / Number of components: 1

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Component #1: protein, Complex I

ProteinName: Complex IRespiratory complex I / Recombinant expression: No
MassExperimental: 970 kDa
SourceSpecies: Ovis aries (sheep)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 90 % / Details: 34s blotting.

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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: 26 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal), 100720.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 3500.0 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: 2600 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 82000
3D reconstructionSoftware: RELION / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL

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