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- EMDB-10013: Cryo-ET on membrane protein -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-10013
TitleCryo-ET on membrane protein
Map data
Sample
  • Complex: Na+/H+ antiporter
Biological speciesBison bison (American bison)
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_10013.png

Downloads & links

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Map

FileDownload / File: emd_10013.map.gz / Format: CCP4 / Size: 78.5 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 13.8 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)4.858849 (±27.59974)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-61-2052
Dimensions860920104
Spacing920860104
CellA: 12696.0 Å / B: 11868.0 Å / C: 1435.2001 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/z920860104
origin x/y/z0.0000.0000.000
length x/y/z12696.00011868.0001435.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-20-6152
NC/NR/NS920860104
D min/max/mean-128.000127.0004.859

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Supplemental data

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Sample components

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Entire : Na+/H+ antiporter

EntireName: Na+/H+ antiporter
Components
  • Complex: Na+/H+ antiporter

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Supramolecule #1: Na+/H+ antiporter

SupramoleculeName: Na+/H+ antiporter / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bison bison (American bison)
Recombinant expressionOrganism: 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: 8
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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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