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Intermediate states observed in the pre-translocation ribosome during tRNA translocation

by single particle reconstruction, at 13.2 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 50, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 50, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5267
TitleIntermediate states observed in the pre-translocation ribosome during tRNA translocation
MapE. coli ribosome: intermediate rotated structure 2
Samplepre-translocation ribosome complex
Keywordsribosome, translocation, tRNA
AuthorsFu J, Munro J, Blanchard SC, Frank J
DateDeposition: 2011-02-25, Header release: 2011-02-28, Map release: 2011-02-28, Last update: 2013-03-06
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 50, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 50, Made by UCSF CHIMERA

Supplemental images
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List of similar structure data about Omokage system
Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 12, Page 4817-21, Year 2011
TitleCryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
AuthorsJie Fu, James B Munro, Scott C Blanchard, Joachim Frank
Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
KeywordsCryoelectron Microscopy (methods), Escherichia coli (chemistry), Mutation, Peptide Chain Elongation, Translational (physiology), RNA, Bacterial (chemistry), RNA, Messenger (chemistry), RNA, Transfer (chemistry, 9014-25-9), Ribosomes (chemistry)
LinksDOI: 10.1073/pnas.1101503108, PubMed: 21383139, PMC: PMC3064370
Map
Fileemd_5267.map.gz ( map file in CCP4 format, 7631 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
125 pix
3 A/pix
= 375. A
125 pix
3 A/pix
= 375. A
125 pix
3 A/pix
= 375. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:50 (by author), 50 (movie #1):
Minimum - Maximum: -85.94808197 - 214.2815094
Average (Standard dev.): 5.23832273 (24.46959686)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions125125125
Origin-62-62-62
Limit626262
Spacing125125125
Unit CellA= B= C: 375 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z333
M x/y/z125125125
origin x/y/z0.0000.0000.000
length x/y/z375.000375.000375.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
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-85.948214.2825.238
Annotation DetailsE. coli ribosome: intermediate rotated structure 2
Supplement
Images
Images
Sample
Namepre-translocation ribosome complex
Number of Components3
Theoretical Mass2.5MDa
Component #1: ribosome-prokaryote - ribosome
Scientific nameribosome
Theoretical Mass2.5 MDa
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
ProkaryoteALL
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Methodblot for 8 seconds
Cryogen NameETHANE
DetailsVitrification instrument: vitrobot
Humidity100
InstrumentFEI VITROBOT
Imaging
MicroscopeFEI POLARA 300
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose24 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 59000, Calibrated: 100000
Astigmatismobjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs2.26 mm
Imaging ModeBRIGHT FIELD
Defocus2500 nm - 4500 nm
Specimen Holder
Holdercartridge
ModelOTHER
Temperature82 K
Camera
DetectorTVIPS TEMCAM-F415 (4k x 4k)
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmreference-based projection matching
SoftwareSPIDER
CTF Correctiondefocus group and wiener filter
Resolution By Author13.2 A
Resolution MethodFSC 0.5
Single Particle
Number of Class Averages4
Applied SymmetryC1 (asymmetric)
Number of Projections84000
Download
Data from EMDB
Header (meta data in XML format)emd-5267.xml (6.4 KB)
Map dataemd_5267.map.gz (1.2 MB)
Imagesemd_5267_1.jpg (153.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5267
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.5 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), 4.9 MB
Session file for UCSF-Chimera, 26.4 KB