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- EMDB-4720: Neurospora crassa cytochrome C oxidase (complex IV) in lipid nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-4720
TitleNeurospora crassa cytochrome C oxidase (complex IV) in lipid nanodisc
Map dataNone
Sample
  • Complex: Complex IV, cytochrome c oxidase
Biological speciesNeurospora crassa (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsBausewein T / Nussberger S / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: IUCrJ / Year: 2019
Title: Cryo-EM structure of respiratory complex IV.
Authors: Thomas Bausewein / Stephan Nussberger / Werner Kühlbrandt /
Abstract: In fungi, the mitochondrial respiratory chain complexes (complexes I-IV) are responsible for oxidative phosphorylation, as in higher eukaryotes. Cryo-EM was used to identify a 200 kDa membrane ...In fungi, the mitochondrial respiratory chain complexes (complexes I-IV) are responsible for oxidative phosphorylation, as in higher eukaryotes. Cryo-EM was used to identify a 200 kDa membrane protein from in lipid nanodiscs as cytochrome oxidase (complex IV) and its structure was determined at 5.5 Å resolution. The map closely resembles the cryo-EM structure of complex IV from . Its ten subunits are conserved in and , but other transmembrane subunits are missing. The different structure of the Cox5a subunit is typical for fungal complex IV and may affect the interaction with complex III in a respiratory supercomplex. Additional density was found between the matrix domains of the Cox4 and Cox5a subunits that appears to be specific to .
History
DepositionMar 22, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseJul 3, 2019-
UpdateJul 31, 2019-
Current statusJul 31, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4720.png

Downloads & links

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Map

FileDownload / File: emd_4720.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 192 pix.
= 209.28 Å		1.09 Å/pix.
x 192 pix.
= 209.28 Å		1.09 Å/pix.
x 192 pix.
= 209.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.0454846 - 0.12714516
Average (Standard dev.)0.00002056974 (±0.004311485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 209.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z209.280209.280209.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0450.1270.000

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Supplemental data

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Sample components

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Entire : Complex IV, cytochrome c oxidase

EntireName: Complex IV, cytochrome c oxidase
Components
  • Complex: Complex IV, cytochrome c oxidase

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Supramolecule #1: Complex IV, cytochrome c oxidase

SupramoleculeName: Complex IV, cytochrome c oxidase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Neurospora crassa (fungus) / Organelle: Mitochondrium

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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

BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Slit width: 70 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2421286
CTF correctionSoftware - Name: Gctf
Startup modelType of model: INSILICO MODEL / In silico model: RELION InitialModel
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0 beta) / Number images used: 134734
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0 beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0 beta)
FSC plot (resolution estimation)

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