EMDB-1127: Mechanism for the disassembly of the posttermination c...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1127
Title	Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
Map	This is a 50S.EF-G.GDPNP.RRF complex from E.coli
Sample	50S.EF-G.GDPNP.RRF complex from E.coli
Authors	Gao N, Zavialov AV, Li W, Sengupta J, Valle M, Gursky RP, Ehrenberg M, Frank J
Date	Deposition: 2005-05-11, Header release: 2005-05-11, Map release: 2006-05-11, Last update: 2012-10-31
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 60, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 60, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-1zn0, PDB-1zn1, Surface level: 60, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-1zn0, Made by Jmol #5: Simplified surface model with fitted atomic model: PDB-1zn1, Made by Jmol
Supplemental images	1127.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-1zn0 CiteFit PDB-1zn1 CiteFit EMDB-1128 Cite Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-1430 EMDB-1019 EMDB-2012 EMDB-1796 EMDB-2171 EMDB-1456 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Mol. Cell, Vol. 18, Issue 6, Page 663-74, Year 2005
Title	Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies.
Authors	Ning Gao, Andrey V Zavialov, Wen Li, Jayati Sengupta, Mikel Valle, Richard P Gursky, Måns Ehrenberg, Joachim Frank Wadsworth Center, State University of New York at Albany, Empire State Plaza, Albany, New York 12201, USA.
Keywords	Cryoelectron Microscopy (methods), Image Processing, Computer-Assisted, Models, Molecular, Molecular Conformation, Peptide Chain Termination, Translational, Peptide Elongation Factor G (metabolism), Protein Conformation, Protein Structure, Secondary, RNA, Messenger (chemistry), Ribosomal Proteins (metabolism), ribosome releasing factor
Links	PII: S1097-2765(05)01311-0, DOI: 10.1016/j.molcel.2005.05.005, PubMed: 15949441

Map

File

EMD-1127.map ( map file in CCP4 format, 8789 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:	55.3, 60 (movie #1):
Minimum - Maximum:	-123.87 - 336.361
Average (Standard dev.):	3.60572 (29.4095)

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	130	130	130
Origin :	-65	-65	-65
Limit :	64	64	64
Spacing :	130	130	130

Unit Cell

A = 366.6 A , B = 366.6 A , C = 366.6 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 2.82 A , Y = 2.82 A , Z = 2.82 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	2.82	2.82	2.82
M x/y/z	130	130	130
origin x/y/z	0.000	0.000	0.000
length x/y/z	366.600	366.600	366.600
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-220	-220	-220
NX/NY/NZ	441	441	441
MAP C/R/S	1	2	3
start NC/NR/NS	-65	-65	-65
NC/NR/NS	130	130	130
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-123.870	336.361	3.606

Annotation Details

This is a 50S.EF-G.GDPNP.RRF complex from E.coli

Supplement
Images
Images	1127.gif

Sample
Name	50S.EF-G.GDPNP.RRF complex from E.coli
Number of Components	3
Component #1: ribosome-prokaryote - 50S subunit
Scientific name	50S subunit
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Prokaryote	LSU 50S
Recombinant expression	No
Component #2: protein - RRF
Scientific name	RRF
Number of Copies	1
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Recombinant expression	No
Component #3: protein - EF-G
Scientific name	EF-G
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Recombinant expression	No

Experiment
Sample Preparation
Staining	Cryo-EM
Specimen Support Details	Quantifoil holley carbon film grids
Specimen State	particle
Buffer	Details: polymix buffer pH: 7.5
Vitrification
Cryogen Name	ETHANE
Humidity	90
Temperature	93 Kelvin
Instrument	HOMEMADE PLUNGER
Method	Blot for 2 seconds before plunging
Details	Vitrification instrument: two-sided blotting plunger
Imaging
Microscope	FEI TECNAI F20
Date	2003-02-01
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	15 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X, Calibrated: 49700 X
Nominal Cs	2.0 mm
Imaging Mode	BRIGHT FIELD
Defocus	1500 nm - 4800 nm
Specimen Holder
Holder	Cryo transfer ( GATAN LIQUID NITROGEN )
Temperature	93 Kelvin
Camera
Detector	Kodak SO163 film
Image Acquisition
Sampling Size	14 microns
Od Range	1.2
Quant Bit Number	12
Scanner	ZEISS SCAI

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	reference projection
Software	SPIDER
CTF Correction	defocus groups
Resolution By Author	15.5
Resolution Method	FSC at 0.5 cut-off
Details	Amplitude correction was applied using low-angle x-ray scattering data.
Single Particle
Number of Projections	32171
Fitted Coordinate
PDB entry ID	PDB-1zn0 PDB-1zn1

Download

Data from EMDB

Header (meta data in XML format)

emd-1127.xml (7.9 KB)

Map data

emd_1127.map.gz (7.9 MB)

Images

1127.gif (30.1 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1127

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, 26.4 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.3 MB .webm (WebM/VP8 format), 4.9 MB Session file for UCSF-Chimera, 26.5 KB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.7 MB .webm (WebM/VP8 format), 5.3 MB Session file for UCSF-Chimera, 268.4 KB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 4.9 MB

movie #5

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5.2 MB