EMDB-1917: Intermediate binding positions of RRF and EF-G on the ...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1917
Title	Intermediate binding positions of RRF and EF-G on the post-termination complex
Map	E. coli 70S post-termination complex with bound Thermus thermophilus RRF and E. coli EF-G.
Sample	T. thermophilus Ribosome Recyling Factor and E. coli Elongation Factor G bound to E. coli Post Termination Complex
Keywords	Ribosome recycling factor, Elongation Factor G, T. thermophilus ribosome recycling factor, 70S, E. coli Post Termination Complex, cryo-EM
Authors	Yokoyama T, Shaikh TR, Iwakura N, Kaji H, Kaji A, Agrawal RK
Date	Deposition: 2011-06-29, Header release: 2011-07-15, Map release: 2012-04-27, Last update: 2012-04-27
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with fitted model, atomic models: PDB-3j0e, Surface level: 272, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 272, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-3j0e, Surface level: 272, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-3j0e, Made by Jmol
Supplemental images	EMD-1917.tif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-3j0e CiteFit EMDB-1915 Cite EMDB-1916 Cite EMDB-1918 Cite PDB-3j0d Cite Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-1248 EMDB-1366 EMDB-1524 EMDB-5266 EMDB-5363 EMDB-5361 List of similar structure data about Omokage system

Article
Citation - Primary
Article	EMBO J., Vol. 31, Issue 7, Page 1836-46, Year 2012
Title	Structural insights into initial and intermediate steps of the ribosome-recycling process.
Authors	Takeshi 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.
Keywords	Cryoelectron 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
Links	DOI: 10.1038/emboj.2012.22, PubMed: 22388519, PMC: PMC3321202

Map

File

EMD-1917.map ( map file in CCP4 format, 8790 KB )

Projections & Slices

Size of images:

Axes	Z (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:	272 (by author), 272 (movie #1):
Minimum - Maximum:	-1350.87719727 - 3122.80712891
Average (Standard dev.):	40.61297226 (297.30963135)

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	130	130	130
Origin :	0	0	0
Limit :	129	129	129
Spacing :	130	130	130

Unit Cell

A = 361.4 A , B = 361.4 A , C = 361.4 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 2.78 A , Y = 2.78 A , Z = 2.78 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	2.78	2.78	2.78
M x/y/z	130	130	130
origin x/y/z	0.000	0.000	0.000
length x/y/z	361.400	361.400	361.400
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	130	130	130
start NC,NX/NR,NY/NS,NZ	0	0	0
NC,NX/NR,NY/NS,NZ	130	130	130
D min/max/mean	-1350.877	3122.807	40.613

Annotation Details

E. coli 70S post-termination complex with bound Thermus thermophilus RRF and E. coli EF-G.

Supplement
Images
Images	EMD-1917.tif

Sample
Name	T. thermophilus Ribosome Recyling Factor and E. coli Elongation Factor G bound to E. coli Post Termination Complex
Number of Components	3
Oligomeric State	Trimer
Theoretical Mass	2.5 MDa
Component #1: ribosome-prokaryote - 70S PoTC
Scientific name	70S E. coli Post-Termination Complex
Common Name	70S PoTC
Theoretical Mass	2.5 MDa
Prokaryote	LSU 50S, SSU 30S
Component #2: protein - RRF
Scientific name	Ribosome Recyling Factor
Common Name	RRF
Scientific Name of Species	Thermus thermophilus (NCBI Taxonomy: 274)
Recombinant expression	Yes
Component #3: protein - EF-G
Scientific name	Elongation Factor G
Common Name	EF-G
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Recombinant expression	Yes

Experiment
Sample Preparation
Specimen Conc	0.08 mg/ml
Specimen Support Details	300 mesh copper grid
Specimen State	particle
Buffer	Details: 50mM Tris-HCl (pH 7.5), 10mM Mg(OAc)2, 25mM KCl pH: 7.5
Vitrification
Cryogen Name	ETHANE
Details	Vitrification instrument: Vitrobot
Humidity	90
Instrument	FEI VITROBOT
Temperature	93 Kelvin
Imaging
Microscope	FEI TECNAI F20
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X, Calibrated: 50310 X
Astigmatism	Objective correct at 200kX mag
Imaging Mode	BRIGHT FIELD
Defocus	400 nm - 4000 nm
Specimen Holder
Holder	Side entry liquid nitrogen cooled cryo holder ( OTHER )
Temperature	80 Kelvin
Camera
Detector	Kodak S0163 Film
Image Acquisition
Scanner	ZEISS SCAI
Number of Digital Images	383
Sampling Size	14 microns
Quant Bit Number	12

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	Projection matching
Software	SPIDER
CTF Correction	each micrograph
Resolution By Author	9.9
Resolution Method	FSC 0.5 cut-off
Single Particle
Number of Projections	338823
Atomic Model Fitting
Model #0
Details	Protocol: Flexible Fitting
Refinement Protocol	flexible
Refinement Space	REAL
Software	MDFF
Model #1
Refinement Space	REAL
Refinement Protocol	flexible
Details	Protocol: Flexible Fitting
Software	MDFF
Model #2
Details	Protocol: Flexible Fitting
Software	MDFF
Refinement Protocol	flexible
Refinement Space	REAL
Fitted Coordinate
PDB entry ID	PDB-3j0e

Download

Data from EMDB

Header (meta data in XML format)

emd-1917.xml (8.8 KB)

Map data

emd_1917.map.gz (1.5 MB)

Images

EMD-1917.tif (278.9 KB)

FTP directory

ftp://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), 3.6 MB .webm (WebM/VP8 format), 5 MB