EMDB-1366: Locking and unlocking of ribosomal motions.

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1366
Title	Locking and unlocking of ribosomal motions.
Map	Cryo-EM map of E.coli 70S ribosome
Sample	EF-G bound Release Complex in the presence of Puromycin and GTP
Authors	Mikel V, Andrey Z, Sengupta J, Rawat U, Ehrenberg M, Frank J
Date	Deposition: 2007-05-22, Header release: 2007-05-24, Map release: 2007-05-24, Last update: 2012-11-07
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 30, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 30, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-1pn6, Surface level: 30, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-1pn6, Made by Jmol #5: Simplified surface model with fitted atomic model: PDB-1pn7, Made by Jmol #6: Simplified surface model with fitted atomic model: PDB-1pn8, Made by Jmol
Supplemental images	1366.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-1pn6 CiteFit PDB-1pn7 CiteFit PDB-1pn8 CiteFit EMDB-1055 Cite EMDB-1362 Cite EMDB-1363 Cite EMDB-1364 Cite EMDB-1365 Cite Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-1395 EMDB-1917 EMDB-1553 EMDB-1248 EMDB-1007 EMDB-1006 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Cell, Vol. 114, Issue 1, Page 123-34, Year 2003
Title	Locking and unlocking of ribosomal motions.
Authors	Mikel Valle, Andrey Zavialov, Jayati Sengupta, Urmila Rawat, Måns Ehrenberg, Joachim Frank Howard Hughes Medical Institute, and Health Research Incororated at the Wadswoth Center, State University of New York, Albany, 12201, USA.
Keywords	Binding Sites (genetics), Cryoelectron Microscopy, Eukaryotic Cells (metabolism), Models, Molecular, Molecular Conformation, Peptide Elongation Factor G (genetics), Peptides (genetics), Protein Biosynthesis (genetics), Protein Structure, Tertiary (genetics), Protein Subunits (genetics), RNA, Messenger (genetics), RNA, Transfer (genetics, 9014-25-9), Ribosomes (genetics), Rotation
Links	PubMed: 12859903, PII: S0092867403004768

Map

File

EMD-1366.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:	57.3, 30 (movie #1):
Minimum - Maximum:	-118.471 - 239.101
Average (Standard dev.):	2.85556 (25.5653)

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= B= C: 366.6 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= 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	-64	-64	-64
NX/NY/NZ	128	128	128
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	-118.471	239.101	2.856

Annotation Details

Cryo-EM map of E.coli 70S ribosome

Supplement
Images
Images	1366.gif

Sample
Name	EF-G bound Release Complex in the presence of Puromycin and GTP
Number of Components	4
Component #1: ribosome-prokaryote - Release Complex
Scientific name	Release Complex
Details	mRNA, tRNA
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Strain	MRE600
Prokaryote	ALL
Recombinant expression	No
Component #2: ligand - Puromycin
Scientific name	Puromycin
Details	Antibiotic
Scientific Name of Species	synthetic construct
NCBI taxonomy	32630
Recombinant expression	No
Component #3: ligand - EF-G
Scientific name	EF-G
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Strain	MRE600
Recombinant expression	No
Component #4: ligand - GTP
Scientific name	GTP
Scientific Name of Species	synthetic construct
NCBI taxonomy	32630
Recombinant expression	No

Experiment
Sample Preparation
Specimen State	particle
Vitrification
Cryogen Name	ETHANE
Details	Rapid-freezing in liquid ethane
Instrument	NONE
Imaging
Microscope	FEI TECNAI F20
Date	11-JUL-2003
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Illumination Mode	FLOOD BEAM
Lens
Imaging Mode	BRIGHT FIELD
Specimen Holder
Holder	cryo transfer
Model	GATAN LIQUID NITROGEN
Tilt Angle	0 degrees - 0 degrees
Temperature	93 K
Camera
Detector	Kodak SO163 film
Image Acquisition
Scanner	ZEISS SCAI
Sampling Size	14

Processing
Method	single particle reconstruction
3D reconstruction
Algorithm	Back projection
Software	SPIDER, package
CTF Correction	CTF correctionn of 3D map
Resolution By Author	12.8 A
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	1
Atomic Model Fitting
Fitted Coordinate
PDB entry ID	PDB-1pn6 PDB-1pn7 PDB-1pn8

Download

Data from EMDB

Header (meta data in XML format)

emd-1366.xml (7.6 KB)

Map data

emd_1366.map.gz (7.8 MB)

Images

1366.gif (61.5 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1366

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, 26.4 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 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), 3.6 MB .webm (WebM/VP8 format), 5 MB Session file for UCSF-Chimera, 229.6 KB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 5 MB

movie #5

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5.1 MB

movie #6

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5 MB