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- EMDB-2676: Electron cryo-microscopy of bovine ComplexI -

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Basic information

Entry
Database: EMDB / ID: 2676
TitleElectron cryo-microscopy of bovine ComplexI
Map dataReconstruction of bovine ComplexI
SampleNADH:ubiquinone oxidoreductase:
KeywordsNADH dehydrogenase / respiratory complex
SourceBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / 4.95 Å resolution
AuthorsVinothkumar KR / Zhu J / Hirst J
CitationJournal: Nature / Year: 2014
Title: Architecture of mammalian respiratory complex I.
Authors: Kutti R Vinothkumar / Jiapeng Zhu / Judy Hirst
Validation ReportPDB-ID: 4uq8

SummaryFull reportAbout validation report
DateDeposition: Jun 13, 2014 / Header (metadata) release: Jul 9, 2014 / Map release: Sep 17, 2014 / Last update: Jul 15, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.32
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.32
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-4uq8
  • Surface level: 0.32
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_2676.map.gz (map file in CCP4 format, 85751 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
280 pix
1.72 Å/pix.
= 480.76 Å
280 pix
1.72 Å/pix.
= 480.76 Å
280 pix
1.72 Å/pix.
= 480.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.717 Å
Density
Contour Level:0.32 (by author), 0.32 (movie #1):
Minimum - Maximum-0.69797403 - 2.63536048
Average (Standard dev.)0.00217741 (0.06465198)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions280280280
Origin000
Limit279279279
Spacing280280280
CellA=B=C: 480.76 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7171.7171.717
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z480.760480.760480.760
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.6982.6350.002

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Supplemental data

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Sample components

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Entire NADH:ubiquinone oxidoreductase

EntireName: NADH:ubiquinone oxidoreductase
Details: The enzyme was isolated from bovine heart mitochondria in detergent micelles and imaged on ice as single particles
Number of components: 1 / Oligomeric State: 1
MassTheoretical: 1000 kDa / Experimental: 1000 kDa

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Component #1: protein, NADH:ubiquinone oxidoreductase

ProteinName: NADH:ubiquinone oxidoreductase / a.k.a: Complex IRespiratory complex I / Oligomeric Details: 1 / Recombinant expression: No / Number of Copies: 1
MassTheoretical: 1000 kDa / Experimental: 1000 kDa
SourceSpecies: Bos taurus (cattle)
Source (natural)Organelle: mitochondria / Location in cell: mitochondrial inner membrane

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3.5 mg/ml / Buffer solution: 20mM Tris-HCl, 150 mM NaCl, 0.03% Cymal-7 / pH: 8
Support film300 mesh holey-carbon Quantifoil gold grid R 0.6/1 glow discharged in air
VitrificationInstrument: OTHER / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 %
Method: The specimen was vitrified in an environmental plunge-freeze apparatus (Bellare et al, J.Electr. Micros. Tech., 1988, 10, 87-111). Blot for 15-18 seconds after the diameter of the blotted meniscus ceases to expand and plunged.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Oct 21, 2013
Details: Exposure intensity set to give 50 electron/pixel/second at the detector, which translates to ~17 electrons/square_Angstrom/second at the specimen. Each image was exposed for 4 seconds.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 64 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 47000 X (nominal), 81495 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification once at the start of data collection
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 5000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 85 K ( 80 - 90 K)
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1154 / Sampling size: 14 microns
Details: An in-house built system was used to intercept the frames from the detector at a rate of 18 frames per second.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 25492 / Details: The particles were manually picked.
3D reconstructionAlgorithm: Relion / Software: Relion / CTF correction: each particle
Details: After extraction and ctf estimation of images, frames 1-32 were used for reconstruction, statistical movie processing to compensate for beam-induced movement and b-factor weighting.
Resolution: 4.95 Å / Resolution method: FSC 0.143, gold-standard
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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