EMDB-5267: Intermediate states observed in the pre-translocation ...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5267
Title	Intermediate states observed in the pre-translocation ribosome during tRNA translocation
Map	E. coli ribosome: intermediate rotated structure 2
Sample	pre-translocation ribosome complex
Keywords	ribosome, translocation, tRNA
Authors	Fu J, Munro J, Blanchard SC, Frank J
Date	Deposition: 2011-02-25, Header release: 2011-02-28, Map release: 2011-02-28, Last update: 2013-03-06
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	[Movies out of date]detail Movie Page #1: Surface view with section colored by density value, Surface level: 50, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 50, Made by UCSF CHIMERA
Supplemental images	EMDB figure
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-5262 Cite EMDB-5265 Cite EMDB-5266 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-5363 EMDB-1524 EMDB-5364 EMDB-1849 EMDB-5265 EMDB-1417 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Proc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 12, Page 4817-21, Year 2011
Title	Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.
Authors	Jie Fu, James B Munro, Scott C Blanchard, Joachim Frank Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
Keywords	Cryoelectron Microscopy (methods), Escherichia coli (chemistry), Mutation, Peptide Chain Elongation, Translational (physiology), RNA, Bacterial (chemistry), RNA, Messenger (chemistry), RNA, Transfer (chemistry, 9014-25-9), Ribosomes (chemistry)
Links	DOI: 10.1073/pnas.1101503108, PubMed: 21383139, PMC: PMC3064370

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 = 375.0 A , B = 375.0 A , C = 375.0 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 3 A , Y = 3 A , Z = 3 A

CCP4 map header info

Annotation Details

E. coli ribosome: intermediate rotated structure 2

Sample
Name	pre-translocation ribosome complex
Number of Components	3
Theoretical Mass	2.5 MDa
Component #1: ribosome-prokaryote - ribosome
Scientific name	ribosome
Theoretical Mass	2.5 MDa
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Prokaryote	ALL
Recombinant expression	No

Experiment
Sample Preparation
Specimen State	particle
Vitrification
Method	blot for 8 seconds
Cryogen Name	ETHANE
Details	Vitrification instrument: vitrobot
Humidity	100
Instrument	FEI VITROBOT
Imaging
Microscope	FEI POLARA 300
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	300 kV
Electron Dose	24 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 59000 X, Calibrated: 100000 X
Astigmatism	objective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs	2.26 mm
Imaging Mode	BRIGHT FIELD
Defocus	2500 nm - 4500 nm
Specimen Holder
Holder	cartridge ( OTHER )
Temperature	82 Kelvin
Camera
Detector	TVIPS F415
Image Acquisition

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	reference-based projection matching
Software	SPIDER
CTF Correction	defocus group and wiener filter
Resolution By Author	13.2
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Class Averages	4
Applied Symmetry	C1 (asymmetric)
Number of Projections	84000

Data from EMDB

Header (meta data in XML format)

Map data

FTP directory

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, 26.3 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, 26.4 KB