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Pretranslocation ribosome. Group after ML3D classification. Racheted ribosome with tRNAs in hybrid positions.

by single particle reconstruction, at 16 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 32, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 32, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1553
TitlePretranslocation ribosome. Group after ML3D classification. Racheted ribosome with tRNAs in hybrid positions.
MapRacheted ribosome with tRNAs in hybrid positions.
Sample70 mRNA tRNAfMet fMetLeu-tRNALeu
Keywordsribosome, pretranslocation, hybrid
AuthorsJulian P, Konevega AL, Scheres SHW, Lazaro M, Gil D, Wintermeyer W, Rodnina MV, Valle M
DateDeposition: 2008-09-08, Header release: 2008-09-15, Map release: 2009-05-05, 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: 32, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 32, Made by UCSF CHIMERA

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

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 105, Issue 44, Page 16924-7, Year 2008
TitleStructure of ratcheted ribosomes with tRNAs in hybrid states.
AuthorsPatricia Julián, Andrey L Konevega, Sjors H W Scheres, Melisa Lázaro, David Gil, Wolfgang Wintermeyer, Marina V Rodnina, Mikel Valle
Structural Biology Unit, Center for Cooperative Research in Biosciences bioGUNE, 48160 Derio, Spain.
KeywordsCryoelectron Microscopy, Models, Molecular, Nucleic Acid Conformation, Peptide Elongation Factor G (chemistry), RNA, Transfer (chemistry, 9014-25-9), RNA, Transfer, Amino Acyl (chemistry), Ribosomes (chemistry), tRNA, peptidyl-
LinksDOI: 10.1073/pnas.0809587105, PubMed: 18971332, PMC: PMC2579354
Map
Fileemd_1553.map.gz ( map file in CCP4 format, 16001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
2.2 A/pix
= 352. A
160 pix
2.2 A/pix
= 352. A
160 pix
2.2 A/pix
= 352. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:32 (by author), 32 (movie #1):
Minimum - Maximum: -81.066 - 192.719
Average (Standard dev.): 3.9672 (24.5844)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin-80-80-80
Limit797979
Spacing160160160
Unit CellA= B= C: 352 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.2 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.22.22.2
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z352.000352.000352.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-81.066192.7193.967
Annotation DetailsRacheted ribosome with tRNAs in hybrid positions.
Supplement
Images
Images
Sample
Name70 mRNA tRNAfMet fMetLeu-tRNALeu
Number of Components3
Component #1: ribosome-prokaryote - pretranslocation ribosome
Scientific name70S E.coli ribosome in the pretranslocation state
Common Namepretranslocation ribosome
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
ProkaryoteALL
Recombinant expressionNo
Experiment
Sample Preparation
StainingcryoEM
Specimen Support DetailsQuantifoil 300 mesh copper
Specimen Stateparticle
BufferDetails: 50 mM Tris-HCl, pH 7.5 30mM KCl 70 mM NH4Cl 20 mM MgCl2 2 mM spermine
pH: 7.5
Vitrification
Methodsingle blot for 1.5 seconds
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Temperature90 Kelvin
Imaging
MicroscopeJEOL 2200FS
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
Holdersingle tilt cryoholder
ModelGATAN LIQUID NITROGEN
Temperature90 K
Camera
DetectorGENERIC GATAN
Image Acquisition
Sampling Size2.2
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmreference matching
SoftwareSPIDER XMIPP
CTF Correctionvolume
Detailssubset after ML3D classification
Resolution By Author16 A
Resolution MethodFSC at 0.15 cut-off
Single Particle
Number of Projections12590
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1553.xml (6.6 KB)
Map dataemd_1553.map.gz (14.5 MB)
Imagesemd_1553.jpg (59.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1553
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, 26.4 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, 26.5 KB