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Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.

by single particle reconstruction, at 11.7 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0003, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.0003, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1s1h, PDB-1s1i, PDB-1trj, Surface level: 0.0003, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1s1h, Image by Jmol

#5: Simplified surface model with fitted atomic model: PDB-1s1i, Image by Jmol

#6: Simplified surface model with fitted atomic model: PDB-1trj, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1067
TitleDomain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
Mapmap
SampleRibosomal 80S-eEF2-sordarin complex from S. cerevisiae
AuthorsSpahn CM, Frank J
DateDeposition: 2004-01-05, Header release: 2004-01-06, Map release: 2005-01-06, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0003, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.0003, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1s1h, PDB-1s1i, PDB-1trj, Surface level: 0.0003, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1s1h, Image by Jmol

#5: Simplified surface model with fitted atomic model: PDB-1s1i, Image by Jmol

#6: Simplified surface model with fitted atomic model: PDB-1trj, Image by Jmol

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-1s1h

CiteFit

PDB-1s1i

CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleEMBO J., Vol. 23, Issue 5, Page 1008-19, Year 2004
TitleDomain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.
AuthorsChristian M T Spahn, Maria G Gomez-Lorenzo, Robert A Grassucci, Rene Jørgensen, Gregers R Andersen, Roland Beckmann, Pawel A Penczek, Juan P G Ballesta, Joachim Frank
Wadsworth Center, Health Research Inc., Howard Hughes Medical Institute, Albany, NY 12201-0509, USA.
KeywordsAntifungal Agents (pharmacology), Cryoelectron Microscopy, Crystallography, X-Ray, Indenes, Models, Molecular, Movement, Nucleic Acid Conformation, Peptide Elongation Factor 2 (chemistry), Protein Binding, Protein Structure, Quaternary, Protein Structure, Tertiary, Protein Subunits (genetics), RNA Transport, RNA, Transfer (chemistry, 9014-25-9), Ribosomes (chemistry), Saccharomyces cerevisiae (chemistry), sordarin (11076-17-8)
LinksPubMed: 14976550, DOI: 10.1038/sj.emboj.7600102, PMC: PMC380967
Map
Fileemd_1067.map.gz ( map file in CCP4 format, 7631 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
125 pix
2.93 A/pix
= 366.25 A
125 pix
2.93 A/pix
= 366.25 A
125 pix
2.93 A/pix
= 366.25 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.000477, 0.0003 (movie #1):
Minimum - Maximum: -0.00084646 - 0.00169185
Average (Standard dev.): 1.69393e-05 (0.00020054)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions125125125
Origin-62-62-62
Limit626262
Spacing125125125
Unit CellA= B= C: 366.25 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.93 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.932.932.93
M x/y/z125125125
origin x/y/z0.0000.0000.000
length x/y/z366.250366.250366.250
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS-62-62-62
NC/NR/NS125125125
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0010.0020.000
Annotation Detailsmap
Supplement
Images
Images
Sample
NameRibosomal 80S-eEF2-sordarin complex from S. cerevisiae
Number of Components2
Theoretical Mass3.2MDa
Component #1: ribosome-eukaryote - 80S ribosome
Scientific name80S ribosome
Scientific Name of SpeciesSaccharomyces cerevisiae

Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
EukaryoteALL
Recombinant expressionNo
Component #2: protein - eEF2
Scientific nameeEF2
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 52000
Astigmatism100,000 X magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderOxford, cryo-transfer 3500
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature93 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Number of Digital Images86
Quant Bit Number12
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmback projection
SoftwareSPIDER
CTF Correctiondefocus group volumes
Resolution By Author11.7 A
Resolution MethodFSC 0.5
Single Particle
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1067.xml (6.9 KB)
Map dataemd_1067.map.gz (7 MB)
Images1067.gif (17.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1067
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.4 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 14.6 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.8 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.1 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.6 MB