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- EMDB-10014: Cryo-ET on yeast respiratory supercomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-10014
TitleCryo-ET on yeast respiratory supercomplex
Map data
Sample
  • Complex: Yeast respiratory supercomplex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodelectron tomography / cryo EM
AuthorsZou XD / Zhao JJ / Xu HY / Carroni M
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Swedish Research Council2012.0112 Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: A simple pressure-assisted method for cryo-EM specimen preparation
Authors: Zou XD / Zhao JJ / Xu HY / Carroni M
History
DepositionJun 2, 2019-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateDec 16, 2020-
Current statusDec 16, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Movie viewer
Supplemental images

emd_10014.png

Downloads & links

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Map

FileDownload / File: emd_10014.map.gz / Format: CCP4 / Size: 82.7 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 13.8 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)0.7187635 (±30.914658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-481441
Dimensions858954106
Spacing954858106
CellA: 13165.2 Å / B: 11840.4 Å / C: 1462.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z13.813.813.8
M x/y/z954858106
origin x/y/z0.0000.0000.000
length x/y/z13165.20011840.4001462.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS14-4841
NC/NR/NS954858106
D min/max/mean-128.000127.0000.719

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Supplemental data

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Sample components

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Entire : Yeast respiratory supercomplex

EntireName: Yeast respiratory supercomplex
Components
  • Complex: Yeast respiratory supercomplex

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Supramolecule #1: Yeast respiratory supercomplex

SupramoleculeName: Yeast respiratory supercomplex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Details: A new freezing method was used called Preassis.
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 50

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