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Locking and unlocking of ribosomal motions.

by single particle reconstruction, at 12.8 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 30, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 30, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1pn6, Surface level: 30, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1pn6, Image by Jmol

#5: Simplified surface model with fitted atomic model: PDB-1pn7, Image by Jmol

#6: Simplified surface model with fitted atomic model: PDB-1pn8, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1366
TitleLocking and unlocking of ribosomal motions.
MapCryo-EM map of E.coli 70S ribosome
SampleEF-G bound Release Complex in the presence of Puromycin and GTP
AuthorsMikel V, Andrey Z, Sengupta J, Rawat U, Ehrenberg M, Frank J
DateDeposition: 2007-05-22, Header release: 2007-05-24, Map release: 2007-05-24, Last update: 2012-11-07
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 30, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 30, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1pn6, Surface level: 30, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1pn6, Image by Jmol

#5: Simplified surface model with fitted atomic model: PDB-1pn7, Image by Jmol

#6: Simplified surface model with fitted atomic model: PDB-1pn8, Image by Jmol

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

PDB-1pn6

CiteFit

PDB-1pn7

CiteFit

PDB-1pn8

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
ArticleCell, Vol. 114, Issue 1, Page 123-34, Year 2003
TitleLocking and unlocking of ribosomal motions.
AuthorsMikel Valle, Andrey Zavialov, Jayati Sengupta, Urmila Rawat, Måns Ehrenberg, Joachim Frank
Howard Hughes Medical Institute, and Health Research Incororated at the Wadswoth Center, State University of New York, Albany, 12201, USA.
KeywordsBinding Sites (genetics), Cryoelectron Microscopy, Eukaryotic Cells (metabolism), Models, Molecular, Molecular Conformation, Peptide Elongation Factor G (genetics), Peptides (genetics), Protein Biosynthesis (genetics), Protein Structure, Tertiary (genetics), Protein Subunits (genetics), RNA, Messenger (genetics), RNA, Transfer (genetics, 9014-25-9), Ribosomes (genetics), Rotation
LinksPubMed: 12859903, PII: S0092867403004768
Map
Fileemd_1366.map.gz ( map file in CCP4 format, 8584 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
2.82 A/pix
= 366.6 A
130 pix
2.82 A/pix
= 366.6 A
130 pix
2.82 A/pix
= 366.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:57.3, 30 (movie #1):
Minimum - Maximum: -118.471 - 239.101
Average (Standard dev.): 2.85556 (25.5653)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions130130130
Origin-65-65-65
Limit646464
Spacing130130130
Unit CellA= B= C: 366.6 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= 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-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-118.471239.1012.856
Annotation DetailsCryo-EM map of E.coli 70S ribosome
Supplement
Images
Images
Sample
NameEF-G bound Release Complex in the presence of Puromycin and GTP
Number of Components4
Component #1: ribosome-prokaryote - Release Complex
Scientific nameRelease Complex
DetailsmRNA, tRNA
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
StrainMRE600
ProkaryoteALL
Recombinant expressionNo
Component #2: ligand - Puromycin
Scientific namePuromycin
DetailsAntibiotic
Scientific Name of Speciessynthetic construct
NCBI taxonomy32630
Recombinant expressionNo
Component #3: ligand - EF-G
Scientific nameEF-G
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
StrainMRE600
Recombinant expressionNo
Component #4: ligand - GTP
Scientific nameGTP
Scientific Name of Speciessynthetic construct
NCBI taxonomy32630
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
DetailsRapid-freezing in liquid ethane
InstrumentNONE
Imaging
MicroscopeFEI TECNAI F20
Date11-JUL-2003
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
Holdercryo transfer
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature93 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerZEISS SCAI
Sampling Size14
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmBack projection
SoftwareSPIDER, package
CTF CorrectionCTF correctionn of 3D map
Resolution By Author12.8 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections1
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1366.xml (7.7 KB)
Map dataemd_1366.map.gz (7.8 MB)
Images1366.gif (61.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1366
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, 26.4 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
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 229.6 KB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5 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), 3.6 MB
.webm (WebM/VP8 format), 5 MB