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- EMDB-4507: Ovine respiratory complex I FRC poor open class -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-4507
TitleOvine respiratory complex I FRC poor open class
Map dataovine mitochondrial respiratory complex I poor open class.
Sample
  • Complex: Ovine mitochondrial respiratory complex I
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsLetts JA / Sazanov LA
Funding support Austria, 1 items
OrganizationGrant numberCountry
European Research Council701309 Austria
CitationJournal: Mol.Cell / Year: 2019
Title: Structures of Respiratory Supercomplex I+III2Reveal Functional and Conformational Crosstalk.
Authors: Letts JA / Fiedorczuk K / Degliesposti G / Skehel M / Sazanov LA
History
DepositionDec 27, 2018-
Header (metadata) releaseAug 21, 2019-
Map releaseAug 21, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_4507.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationovine mitochondrial respiratory complex I poor open class.
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.14985788 - 0.49769443
Average (Standard dev.)0.00001083369 (±0.012568832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 716.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z716.800716.800716.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.1500.4980.000

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Supplemental data

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Sample components

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Entire : Ovine mitochondrial respiratory complex I

EntireName: Ovine mitochondrial respiratory complex I
Components
  • Complex: Ovine mitochondrial respiratory complex I

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Supramolecule #1: Ovine mitochondrial respiratory complex I

SupramoleculeName: Ovine mitochondrial respiratory complex I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#44
Details: Poor open class from ovine mitochondrial respiratory complex I
Source (natural)Organism: Ovis aries (sheep) / Organ: Heart / Tissue: Cardiac / Organelle: Mitochondria / Location in cell: Mitochondrial inner membrane
Molecular weightTheoretical: 1.4 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
0.25 MNaClsodium chloride
0.02 MHEPES
0.02 %Brij-35

Details: 250 mM NaCl, 20 mM HEPES, pH 7.7, 0.02% Brij-35
VitrificationCryogen name: PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: blotting for 30 seconds at 4 degrees Celsius, 95% humidity and flash freezing.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number grids imaged: 1 / Number real images: 1854 / Average exposure time: 2.0 sec. / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 100000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 400000
CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5lnk

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 11191
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2)

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