EMDB-1055: Locking and unlocking of ribosomal motions.

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1055
Title	Locking and unlocking of ribosomal motions.
Map	70S + fMet-tRNA + PhetRNA + EF-Tu + GDP + kir mRNA codes for MP-stop
Sample	70S ribosome from E. coli complex 70S-fMet-tRNA-Phe-tRNA-EF-Tu-GDP-kirromycin.
Authors	Valle M, Zavialov A, Li W, Stagg SM, Sengupta J, Nielsen RC, Nissen P, Hervey SC, Ehrenberg M, Frank J
Date	Deposition: 2003-09-22, Header release: 2003-09-29, Map release: 2004-01-06, Last update: 2012-10-24
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, PDB-1pn7, PDB-1pn8, 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	1055.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-1362 Cite EMDB-1363 Cite EMDB-1364 Cite EMDB-1365 Cite EMDB-1366 Cite PDB-1qza PDB-1qzd PDB-1r2x PDB-3e1a PDB-3e1b PDB-3e1c PDB-3e1d Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-1615 EMDB-1363 EMDB-1006 EMDB-1541 EMDB-5364 EMDB-1310 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-1055.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:	57.2, 30 (movie #1):
Minimum - Maximum:	-85.8589 - 250.984
Average (Standard dev.):	4.44442 (25.344)

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	0	0	52
NX/NY/NZ	128	128	55
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	-85.859	250.984	4.444

Annotation Details

70S + fMet-tRNA + PhetRNA + EF-Tu + GDP + kir mRNA codes for MP-stop

Supplement
Images
Images	1055.gif

Sample
Name	70S ribosome from E. coli complex 70S-fMet-tRNA-Phe-tRNA-EF-Tu-GDP-kirromycin.
Number of Components	5
Component #1: ribosome-prokaryote - ribosome
Scientific name	70S from E. coli
Common Name	ribosome
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Prokaryote	ALL
Recombinant expression	No
Component #2: nucleic-acid - trna
Scientific name	fMet-tRNAfMet
Common Name	trna
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Synthetic	No
Structure	DOUBLE HELIX
Class	RNA
Component #3: nucleic-acid - trna
Scientific name	Phe-tRNAPhe
Common Name	trna
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Class	RNA
Synthetic	No
Structure	DOUBLE HELIX
Component #4: protein - Elongation Factor
Scientific name	Elongation Factor Tu
Common Name	Elongation Factor
Number of Copies	1
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Recombinant expression	No
Component #5: nucleic-acid - trna
Scientific name	deacylated tRNA
Common Name	trna
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Synthetic	No
Class	RNA
Structure	DOUBLE HELIX

Experiment
Sample Preparation
Staining	Cryo-electron microscopy. No stain.
Specimen Support Details	300 mesh Quantifoil R2/4
Specimen State	particle
Buffer	Details: 5 mM potassium phosphate, 5 mM magnesium acetate, 5 mM ammonium chloride, 95 mM potassium chloride, 0.5 mM calcium chloride, 8 mM putrescine, 1 mM spermidine, and 1 mM dithioerythritol pH: 7.5
Vitrification
Cryogen Name	ETHANE
Temperature	90 Kelvin
Method	two-face blotting for 1 second
Imaging
Microscope	FEI TECNAI F20
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, Calibrated: 49650
Astigmatism	corrected at 175,000
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	2000 nm - 4000 nm
Specimen Holder
Holder	single tilt cryoholder
Model	GATAN LIQUID NITROGEN
Tilt Angle	0 degrees - 0 degrees
Temperature	90 K
Camera
Detector	Kodak SO163 film
Image Acquisition
Number of Digital Images	50
Sampling Size	14
Od Range	1
Quant Bit Number	16
Scanner	ZEISS SCAI

Processing
Method	single particle reconstruction
3D reconstruction
Algorithm	Reference-based alignement
Software	Spider
CTF Correction	segregation in defocus groups and correction in volumes
Resolution By Author	9 A
Resolution Method	FSC cut-off at 0.15
Single Particle
Number of Projections	75996
Atomic Model Fitting
Model #0
Refinement Protocol	rigid body
Target Criteria	correlation coeficient
Software	O
Details	Protocol: rigid body. Manual fitting in O.The docking of X-ray structures into the cryo-EM maps was made using O and the visualization was performed in IRIS Explorer. EF-G domains were taken from the Thermus thermophilus H573A mutant crystal structure in complex with GDP (PDB code: 1FNM). The coordinates of the ribosomal proteins and rRNAs were taken from published atomic structures (PDB code 1FFK for the 50S subunit; 1FJF for the 30S subunit and the docking was performed using the coordinates as rigid bodies.
PDB Entry ID	1FNM, 1FFK, 1FJF PDB-1fnm PDB-1ffk PDB-1fjf
Fitted Coordinate
PDB entry ID	PDB-1pn6 PDB-1pn7 PDB-1pn8

Download

Data from EMDB

Header (meta data in XML format)

emd-1055.xml (10 KB)

Map data

emd_1055.map.gz (7.8 MB)

Images

1055.gif (80.1 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1055

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), 3.3 MB .webm (WebM/VP8 format), 5.1 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, 277.4 KB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5.3 MB

movie #5

	.mp4 (H.264/MPEG-4 AVC format), 3.7 MB .webm (WebM/VP8 format), 5.3 MB

movie #6

	.mp4 (H.264/MPEG-4 AVC format), 3.7 MB .webm (WebM/VP8 format), 5.2 MB