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Intermediate binding positions of RRF and EF-G on the post-termination complex

by single particle reconstruction, at 9.9 A resolution

Movie

Orientation:

#1: Surface view with fitted model, atomic models: PDB-3j0e, Surface level: 272, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 272, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j0e, Surface level: 272, Image by UCSF CHIMERA

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

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1917
TitleIntermediate binding positions of RRF and EF-G on the post-termination complex
MapE. coli 70S post-termination complex with bound Thermus thermophilus RRF and E. coli EF-G.
SampleT. thermophilus Ribosome Recyling Factor and E. coli Elongation Factor G bound to E. coli Post Termination Complex
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: 2011-07-15, Map release: 2012-04-27, Last update: 2014-09-10
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with fitted model, atomic models: PDB-3j0e, Surface level: 272, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 272, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j0e, Surface level: 272, Image by UCSF CHIMERA

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

Supplemental images
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Related Structure Data
Related Entries

PDB-3j0e

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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_1917.map.gz ( map file in CCP4 format, 8584 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
130 pix
2.78 A/pix
= 361.4 A
130 pix
2.78 A/pix
= 361.4 A
130 pix
2.78 A/pix
= 361.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:272 (by author), 272 (movie #1):
Minimum - Maximum: -1350.87719727 - 3122.80712891
Average (Standard dev.): 40.61297226 (297.30963135)
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-184-184-183
NX/NY/NZ368368368
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-1350.8773122.80740.613
Annotation DetailsE. coli 70S post-termination complex with bound Thermus thermophilus RRF and E. coli EF-G.
Supplement
Images
Images
Sample
NameT. thermophilus Ribosome Recyling Factor and E. coli Elongation Factor G bound to E. coli Post Termination Complex
Number of Components3
Oligomeric StateTrimer
Theoretical Mass2.5MDa
Component #1: ribosome-prokaryote - 70S PoTC
Scientific name70S E. coli Post-Termination Complex
Common Name70S PoTC
Theoretical Mass2.5 MDa
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
ProkaryoteLSU 50S, SSU 30S
Recombinant expressionNo
Component #2: protein - RRF
Scientific nameRibosome Recyling Factor
Common NameRRF
Scientific Name of SpeciesThermus thermophilus
NCBI taxonomy274
Recombinant expressionYes
Component #3: protein - EF-G
Scientific nameElongation Factor G
Common NameEF-G
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
Recombinant expressionYes
Experiment
Sample Preparation
Specimen Conc0.08 mg/ml
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 200kX mag
Imaging ModeBRIGHT FIELD
Defocus400 nm - 4000 nm
Specimen Holder
HolderSide entry liquid nitrogen cooled cryo holder
ModelOTHER
Temperature80 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
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
Single Particle
Number of Projections338823
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
DetailsProtocol: Flexible Fitting
Refinement Protocolflexible
Refinement SpaceREAL
SoftwareMDFF
PDB Entry ID2AVY
Model #1
Refinement SpaceREAL
Refinement Protocolflexible
DetailsProtocol: Flexible Fitting
SoftwareMDFF
PDB Entry ID2AW4
Model #2
DetailsProtocol: Flexible Fitting
SoftwareMDFF
Refinement Protocolflexible
Refinement SpaceREAL
PDB Entry ID1EH1
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1917.xml (9.1 KB)
Map dataemd_1917.map.gz (1.5 MB)
ImagesEMD-1917.tif (278.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1917
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, 2.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 27 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.4 MB
Session file for UCSF-Chimera, 2.5 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 3.4 MB