EMDB-1553: Pretranslocation ribosome. Group after ML3D classifica...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1553
Authors	Julian P, Konevega AL, Scheres SHW, Lazaro M, Gil D, Wintermeyer W, Rodnina MV, Valle M
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 32, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 32, Made by UCSF CHIMERA
Supplemental images	emd_1553.jpg
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-1551 Cite EMDB-1554 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-1726 EMDB-1366 EMDB-1064 EMDB-1722 EMDB-1551 EMDB-1395 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Proc. Natl. Acad. Sci. U.S.A., Vol. 105, Issue 44, Page 16924-7, Year 2008
Title	Structure of ratcheted ribosomes with tRNAs in hybrid states.
Authors	Patricia Julián, Andrey L Konevega, Sjors H W Scheres, Melisa Lázaro, David Gil, Wolfgang Wintermeyer, Marina V Rodnina, Mikel Valle Structural Biology Unit, Center for Cooperative Research in Biosciences bioGUNE, 48160 Derio, Spain.
Keywords	Cryoelectron Microscopy, Models, Molecular, Nucleic Acid Conformation, Peptide Elongation Factor G (chemistry), RNA, Transfer (chemistry, 9014-25-9), RNA, Transfer, Amino Acyl (chemistry), Ribosomes (chemistry), tRNA, peptidyl-
Links	DOI: 10.1073/pnas.0809587105, PubMed: 18971332, PMC: PMC2579354

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A = 352 A , B = 352 A , C = 352 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 2.2 A , Y = 2.2 A , Z = 2.2 A

CCP4 map header info

Annotation Details

Racheted ribosome with tRNAs in hybrid positions.

Sample
Name	70 mRNA tRNAfMet fMetLeu-tRNALeu
Number of Components	3
Component #1: ribosome-prokaryote - pretranslocation ribosome
Scientific name	70S E.coli ribosome in the pretranslocation state
Common Name	pretranslocation ribosome
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Prokaryote	ALL
Recombinant expression	No

Experiment
Sample Preparation
Staining	cryoEM
Specimen Support Details	Quantifoil 300 mesh copper
Specimen State	particle
Buffer	Details: 50 mM Tris-HCl, pH 7.5 30mM KCl 70 mM NH4Cl 20 mM MgCl2 2 mM spermine pH: 7.5
Vitrification
Method	single blot for 1.5 seconds
Cryogen Name	ETHANE
Details	Vitrification instrument: Vitrobot
Humidity	100
Instrument	FEI VITROBOT
Temperature	90 Kelvin
Imaging
Microscope	OTHER
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	10 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Nominal Cs	2.0 mm
Imaging Mode	BRIGHT FIELD
Specimen Holder
Holder	single tilt cryoholder ( GATAN LIQUID NITROGEN )
Temperature	90 Kelvin
Camera
Detector	CCD Gatan camera
Image Acquisition
Sampling Size	2.2 microns

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	reference matching
Software	SPIDER XMIPP
CTF Correction	volume
Details	subset after ML3D classification
Resolution By Author	16
Resolution Method	FSC at 0.15 cut-off
Single Particle
Number of Projections	12590

Data from EMDB

Header (meta data in XML format)

Map data

Images

FTP directory

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), 3.2 MB .webm (WebM/VP8 format), 4.9 MB Session file for UCSF-Chimera, 26.5 KB