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

by single particle reconstruction, at 11 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 35, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 35, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1726
TitleRibosome dynamics and tRNA movement as visualized by time-resolved electron cryomicroscopy
MapAverage map of E. coli 70S-fMetVal-tRNAVal post-translocation complex prepared at 4 degrees C
SampleE. coli 70S-fMetVal-tRNAVal post-translocation complex at 4 degrees C
KeywordsRibosome, translation, translocation, tRNA
AuthorsFischer N, Konevega AL, Wintermeyer W, Rodnina MV, Stark H
DateDeposition: 2010-04-30, Header release: 2010-06-15, Map release: 2011-05-06, 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: 35, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 35, Image by UCSF CHIMERA

Supplemental images
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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
3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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_1726.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:35 (by author), 35 (movie #1):
Minimum - Maximum: -117.661 - 211.522
Average (Standard dev.): -0.507737 (21.8951)
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-117.661211.522-0.508
Annotation DetailsAverage map of E. coli 70S-fMetVal-tRNAVal post-translocation complex prepared at 4 degrees C
Supplement
Images
Images
Sample
NameE. coli 70S-fMetVal-tRNAVal post-translocation complex at 4 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 4 degrees C
Humidity40
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 Author11 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections16893
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1726.xml (7.9 KB)
Map dataemd_1726.map.gz (25 MB)
Imagesimage1726.png (183.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1726
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.8 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.9 KB