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Sub-tomogram average of cytosolic yeast polysomes associated with mitochondria

by subtomogram averaging, at 46 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 143, Imaged by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 143, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 3763
TitleSub-tomogram average of cytosolic yeast polysomes associated with mitochondria
MapSub-tomogram average of cytosolic yeast polysomes associated with mitochondria
SampleS. cerevisiae cytosolic polyribosome associated with mitochondria
AuthorsGold VAM, Chroscicki P, Bragoszewski P, Chacinska A
DateDeposition: 2017-06-14, Header release: 2017-06-28, Map release: 2017-08-30, Last update: 2017-09-06
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 143, Imaged by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 143, Imaged by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleEMBO Rep., Year 2017
TitleVisualization of cytosolic ribosomes on the surface of mitochondria by electron cryo-tomography.
AuthorsVicki Am Gold, Piotr Chroscicki, Piotr Bragoszewski, Agnieszka Chacinska
Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
Living Systems Institute, University of Exeter, Exeter, UK.
College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Exeter, UK.
The International Institute of Molecular and Cell Biology, Warsaw, Poland.
The International Institute of Molecular and Cell Biology, Warsaw, Poland
Centre of New Technologies, University of Warsaw, Warsaw, Poland.
LinksPubMed: 28827470, DOI: 10.15252/embr.201744261
Map
Fileemd_3763.map.gz ( map file in CCP4 format, 2049 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
80 pix
6.7 A/pix
= 536. A
80 pix
6.7 A/pix
= 536. A
80 pix
6.7 A/pix
= 536. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:142 (by author), 143 (movie #1):
Minimum - Maximum: 134.00002 - 148.99998
Average (Standard dev.): 140.56647 (1.3885281)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions808080
Origin000
Limit797979
Spacing808080
Unit CellA= B= C: 536 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 6.7 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z6.76.76.7
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z536.000536.000536.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean134.000149.000140.566
Annotation DetailsSub-tomogram average of cytosolic yeast polysomes associated with mitochondria
Supplement
Images
Images
Sample
NameS. cerevisiae cytosolic polyribosome associated with mitochondria
Number of Components1
Component #1: protein - S. cerevisiae cytosolic polyribosome associated with mitochondria
Scientific nameS. cerevisiae cytosolic polyribosome associated with mitochondria
Scientific Name of SpeciesSaccharomyces cerevisiae

NCBI taxonomy4932
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
BufferpH: 7.2
Vitrification
Cryogen NameETHANE
Detailsblotted for ~4 s on one side in a humidified atmosphere
Imaging
MicroscopeFEI TITAN KRIOS
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose2 e/A**2
Illumination ModeFLOOD BEAM
Lens
Imaging ModeBRIGHT FIELD
Defocus5000 nm - 8000 nm
Specimen Holder
ModelOTHER
Camera
DetectorGATAN K2 (4k x 4k)
Processing
Methodsubtomogram averaging
3D reconstruction
SoftwareIMOD
Resolution By Author46 A
Resolution MethodFSC 0.5 CUT-OFF
Subtomogram Averaging
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-3763-v19.xml (5.3 KB)
emd-3763-v20.xml (7.5 KB)
emd-3763.xml (5.3 KB)
Map dataemd_3763.map.gz (1.5 MB)
Imagesemd_3763.png (98.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-3763
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 7.6 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 8 MB
Session file for UCSF-Chimera, 26.5 KB