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A 12.6A cryo-EM map of the 80S.eEF2.AlF4-GDP complex

by single particle reconstruction, at 12.6 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 54.938231753, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 54.938231753, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5015
AuthorsSengupta J, Nilsson J, Gursky R, Kjeldgaard M, Nissen P, Frank J
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 54.938231753, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 54.938231753, Made by UCSF CHIMERA

Supplemental images

EMDB figure
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Diagram

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Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 382, Issue 1, Page 179-87, Year 2008
TitleVisualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy.
AuthorsJayati Sengupta, Jakob Nilsson, Richard Gursky, Morten Kjeldgaard, Poul Nissen, Joachim Frank
Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA.
KeywordsAluminum Compounds (pharmacology), Cryoelectron Microscopy, Fluorides (pharmacology), Fungal Proteins (chemistry), Guanosine Diphosphate (metabolism, 146-91-8), Guanosine Triphosphate (metabolism, 86-01-1), Hydrolysis (drug effects), Models, Molecular, Peptide Elongation Factor 2 (chemistry), Protein Structure, Tertiary, Ribosomes (drug effects), tetrafluoroaluminate (21340-02-3)
LinksPII: S0022-2836(08)00834-6, DOI: 10.1016/j.jmb.2008.07.004, PubMed: 18644383, PMC: PMC2990977
Map
FileEMD-5015.map ( map file in CCP4 format, 8790 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:65.2 (by author), 54.9382318 (movie #1):
Minimum - Maximum: -115.04087830 - 227.62266541
Average (Standard dev.): 4.20576191 (25.47189331)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 130 130 130
Origin : 0 0 0
Limit : 129 129 129
Spacing : 130 130 130
Unit CellA = 366.6 A , B = 366.6 A , C = 366.6 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 2.82 A , Y = 2.82 A , Z = 2.82 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.822.822.82
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z366.600366.600366.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-115.041227.6234.206
Annotation DetailsCryo-EM reconstruction of 80S.eEF2 complex captured in transition state
Supplement
Sample
NameThe eEF2-bound 80S ribosome in the presence of aluminum fluoride (AlF4-) and GDP
Number of Components4
DetailsAlF4- mimicking the g-phosphate during hydrolysis
Component #1: ribosome-eukaryote - 80S ribosome
Scientific name80S ribosome
Scientific Name of SpeciesThermomyces lanuginosus (NCBI Taxonomy: 5541)
EukaryoteALL
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
Specimen Support DetailsQuantifoil grid
BufferDetails: 20 mM Hepes-NH3, 100 mM KCl, 20 mM MgCl2
pH: 7.2
Vitrification
Cryogen NameNITROGEN
DetailsVitrification instrument: Vitrobot
Humidity90
InstrumentFEI VITROBOT
Temperature93 Kelvin
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000 X,
Imaging ModeBRIGHT FIELD
Defocus1500 nm - 4500 nm
Specimen Holder
HolderSingle tilt cyro-holder ( GATAN LIQUID NITROGEN )
Camera
Image Acquisition
Sampling Size2.82 microns
Quant Bit Number16
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmSingle particle
SoftwareSpider
CTF CorrectionSegregation in defocus groups and correction in volumes
DetailsSupervised Classification was used
Resolution By Author12.6
Resolution MethodFSC at 0.5 cut-off
Single Particle
Applied SymmetryC1 (asymmetric)
Number of Projections28242
DetailsThe image processing using SPIDER included a 3D projection alignment procedure with correction of the contrast transfer function and enhancement of the high-resolution Fourier amplitudes based on X-ray solution scattering data.
Atomic Model Fitting
Model #0
Target Criteriacorrelation coefficient
DetailsThe domains were separately fitted by manual docking using program O
Refinement Protocolrigid body
Refinement SpaceREAL
Download
Data from EMDB
Header (meta data in XML format)emd-5015.xml (7.1 KB)
Map dataemd_5015.map.gz (7.9 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5015
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, 19.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 19.7 KB