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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, Image by UCSF CHIMERA

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

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5265
TitleIntermediate states observed in the pre-translocation ribosome during tRNA translocation
MapE. coli ribosome: rotated structure
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, Image by UCSF CHIMERA

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

Supplemental images
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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
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_5265.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: -124.09147644 - 251.13751221
Average (Standard dev.): 4.70021105 (26.03857613)
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-124.091251.1384.700
Annotation DetailsE. coli ribosome: rotated structure
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-5265.xml (6.3 KB)
Map dataemd_5265.map.gz (1.2 MB)
Imagesemd_5265_1.jpg (156.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5265
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 3.6 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 3.1 MB
Session file for UCSF-Chimera, 26.4 KB