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Ribosome dynamics and tRNA movement as visualized by time-resolved electron cryomicroscopy

by single particle reconstruction, at 9 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 40, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 40, Image by UCSF CHIMERA

#3: Simplified surface model with fitted atomic model: PDB-4v7a, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1724
TitleRibosome dynamics and tRNA movement as visualized by time-resolved electron cryomicroscopy
MapSubstate of E. coli 70S-fMetVal-tRNAVal post-translocation complex at 18 degrees C
SampleSubstate of E. coli 70S-fMetVal-tRNAVal post-translocation complex at 18 degrees C
KeywordsRibosome, translation, translocation, tRNA
AuthorsFischer N, Konevega AL, Wintermeyer W, Rodnina MV, Stark H
DateDeposition: 2010-04-30, Header release: 2010-05-13, Map release: 2011-05-06, Last update: 2014-01-29
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 40, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 40, Image by UCSF CHIMERA

#3: Simplified surface model with fitted atomic model: PDB-4v7a, Image by Jmol

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

Cite: data citing same article

Fit: output model of fitting

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Article
Citation - Primary
ArticleNature, Vol. 466, Issue 7304, Page 329-33, Year 2010
TitleRibosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.
AuthorsNiels Fischer, Andrey L Konevega, Wolfgang Wintermeyer, Marina V Rodnina, Holger Stark
KeywordsCryoelectron Microscopy, Escherichia coli, Kinetics, Models, Molecular, Molecular Conformation, Movement, Protein Biosynthesis, RNA, Transfer (genetics, 9014-25-9), Ribosome Subunits, Large, Bacterial (chemistry), Ribosome Subunits, Small, Bacterial (chemistry), Ribosomes (chemistry), Temperature, Thermodynamics, Time Factors
LinksDOI: 10.1038/nature09206, PubMed: 20631791
Map
Fileemd_1724.map.gz ( map file in CCP4 format, 27649 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.87 A/pix
= 359.04 A
192 pix
1.87 A/pix
= 359.04 A
192 pix
1.87 A/pix
= 359.04 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:40 (by author), 40 (movie #1):
Minimum - Maximum: -122.023 - 223.953
Average (Standard dev.): -0.755981 (22.4777)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin000
Limit191191191
Spacing192192192
Unit CellA= B= C: 359.04 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.87 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.871.871.87
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z359.040359.040359.040
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-122.023223.953-0.756
Annotation DetailsSubstate of E. coli 70S-fMetVal-tRNAVal post-translocation complex at 18 degrees C
Supplement
Images
Images
Sample
NameSubstate of E. coli 70S-fMetVal-tRNAVal post-translocation complex at 18 degrees C
Number of Components3
Theoretical Mass2.5MDa
Component #1: ribosome-prokaryote - E. coli 70S
Scientific nameRibosome
Common NameE. coli 70S
Theoretical Mass2.5 MDa
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
ProkaryoteALL
Recombinant expressionNo
Component #2: nucleic-acid - peptidyl tRNA
Scientific namefMetVal-tRNAVal
Common Namepeptidyl tRNA
Theoretical Mass0.025 MDa
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
ClassT-RNA
StructureDOUBLE HELIX
SyntheticNo
Component #3: nucleic-acid - mRNA
Scientific namem022 mRNA
Common NamemRNA
DetailsCoding sequence AUGGUU
Scientific Name of Speciessynthetic construct
NCBI taxonomy32630
ClassRNA
StructureSINGLE STRANDED
SyntheticYes
Experiment
Sample Preparation
Specimen Stateparticle
BufferDetails: 50 mM Tris-HCl, 70 mM NH4Cl, 30 mM KCl, 7 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
pH: 7.5
Vitrification
MethodManual blotting for about 2 seconds
Cryogen NameETHANE
DetailsVitrification instrument: Custom-built CEVS. Dew-point temperature (temperature on the grid) adjusted to 18 degrees C
Humidity75
InstrumentHOMEMADE PLUNGER
Temperature77 Kelvin
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage160 kV
Electron Dose20 e/A**2
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 161000, Calibrated: 162740
AstigmatismObjective lens astigmatism was corrected at 200,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus500 nm - 2000 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Temperature77 K
Camera
DetectorGENERIC TVIPS (4k x 4k)
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection matching
SoftwareIMAGIC, custom, Spider
CTF CorrectionLocal
Resolution By Author9 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections26429
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1724.xml (8 KB)
Map dataemd_1724.map.gz (25 MB)
Imagesimage1724.png (203.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1724
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, 26.3 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, 26.9 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 305.4 KB
.webm (WebM/VP8 format) [no file]