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Binding conformations and positions of RRF and EF-G during intermediate state of ribosome recycling

by single particle reconstruction, at 9.9 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 13, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 13, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j0e, Surface level: 13, Made by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-3j0e, Made by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1918
TitleBinding conformations and positions of RRF and EF-G during intermediate state of ribosome recycling
MapT. thermophilus Ribosome Recycling Factor and E. coli Elongation Factor G
SampleT. thermophilus Ribosome Recycling Factor and E. coli Elongation Factor G
KeywordsRibosome recycling factor, Elongation Factor G, T. thermophilus ribosome recycling factor, 70S, E. coli Post-Termination Complex, cryo-EM
AuthorsYokoyama T, Shaikh TR, Iwakura N, Kaji H, Kaji A, Agrawal RK
DateDeposition: 2011-06-29, Header release: 2011-07-22, Map release: 2012-04-27, Last update: 2012-05-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 13, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 13, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j0e, Surface level: 13, Made by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-3j0e, Made by Jmol

Supplemental images

EMD-1918.tif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-3j0e
CiteFit

EMDB-1915
Cite

EMDB-1916
Cite

EMDB-1917
Cite

PDB-3j0d
Cite

Cite: data citing same article

Fit: output model of fitting

Similar strucutres (beta)

Diagram

PDB-3ixz

PDB-3j2p

PDB-1kvp

PDB-2ix8
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleEMBO J., Vol. 31, Issue 7, Page 1836-46, Year 2012
TitleStructural insights into initial and intermediate steps of the ribosome-recycling process.
AuthorsTakeshi Yokoyama, Tanvir R Shaikh, Nobuhiro Iwakura, Hideko Kaji, Akira Kaji, Rajendra K Agrawal
Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY, USA.
KeywordsCryoelectron Microscopy, Escherichia coli (metabolism), Escherichia coli Proteins (metabolism), L11 protein, E coli, Peptide Elongation Factor G (metabolism), Protein Binding, Protein Conformation, RNA, Ribosomal (metabolism), Ribosomal Proteins (metabolism), Ribosomes (metabolism), ribosome releasing factor
LinksDOI: 10.1038/emboj.2012.22, PubMed: 22388519, PMC: PMC3321202
Map
FileEMD-1918.map ( map file in CCP4 format, 8790 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:6.43 (by emdb), 13 (movie #1):
Minimum - Maximum: -9.11933231 - 57.06096649
Average (Standard dev.): 0.1077323 (1.93141139)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions130130130
Origin000
Limit129129129
Spacing130130130
Unit CellA= B= C: 361.4 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.78 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.782.782.78
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z361.400361.400361.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-9.11957.0610.108
Annotation DetailsT. thermophilus Ribosome Recycling Factor and E. coli Elongation Factor G
Supplement
Images
Images

EMD-1918.tif
Sample
NameT. thermophilus Ribosome Recycling Factor and E. coli Elongation Factor G
Number of Components2
Oligomeric StateMonomer
Theoretical Mass0.1MDa
Component #1: protein - ttRRF
Scientific nameT. thermophilus Ribosome Recycling Factor
Common NamettRRF
Theoretical Mass0.1 MDa
DetailsThis is the excised density corresponding to Thermus thermophilus RRF and E. coli EF-G from the parent map EMD-1917.
Scientific Name of SpeciesThermus thermophilus
NCBI taxonomy274
Recombinant expressionYes
Engineered SourceExpression system: Escherichia coli JM109
Vector: pGEM-T
Component #2: protein - ecEFG
Scientific nameE. coli Elongation Factor G
Common NameecEFG
Theoretical Mass0.1 MDa
DetailsThis is the excised density corresponding to Thermus thermophilus RRF and E. coli EF-G from the parent map EMD-1917.
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
Recombinant expressionYes
Engineered SourceVector: pUC3G
Expression system: Escherichia coli JM83
Experiment
Sample Preparation
Specimen Support Details300 mesh copper grid
Specimen Stateparticle
BufferDetails: 50mM Tris-HCl (pH 7.5), 10mM Mg(OAc)2, 25mM KCl
pH: 7.5
Vitrification
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity90
InstrumentFEI VITROBOT
Temperature93 Kelvin
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 50310
AstigmatismObjective correct at 200,000 times magnification
Imaging ModeBRIGHT FIELD
Defocus400 nm - 4000 nm
Specimen Holder
HolderSide entry liquid nitrogen cooled cryo holder
ModelOTHER
Temperature80 K
Camera
DetectorKodak S0163 Film
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images383
Sampling Size14
Quant Bit Number12
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection matching
SoftwareSPIDER
CTF Correctioneach micrograph
Resolution By Author9.9 A
Resolution MethodFSC 0.5 cut-off
Single Particle
Number of Projections338823
Atomic Model Fitting
Model #0
DetailsProtocol: Flexible Fitting
SoftwareMDFF
Refinement Protocolflexible
Refinement SpaceREAL
PDB Entry ID1eh1

PDB-1eh1
Fitted Coordinate
PDB entry ID

PDB-3j0e
Download
Data from EMDB
Header (meta data in XML format)emd-1918.xml (8.3 KB)
Map dataemd_1918.map.gz (63.3 KB)
ImagesEMD-1918.tif (115.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1918
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.4 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), 4.6 MB
Session file for UCSF-Chimera, 26.7 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 930 KB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.9 MB