EMDB-1091: Cryo-EM visualization of a viral internal ribosome ent...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1091
Title	Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
Map	map
Sample	Human ribosome 80S bound with CrPV IRES
Authors	Spahn CM, Frank J
Date	Deposition: 2004-08-10, Header release: 2004-08-10, Map release: 2004-11-10, Last update: 2012-10-17
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 0.0003, Made by UCSF CHIMERA #2: Surface view colored by height, Surface level: 0.0003, Made by UCSF CHIMERA
Supplemental images	1091.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-1090 Cite EMDB-1092 Cite EMDB-1093 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-1670 EMDB-1198 EMDB-5225 EMDB-1528 EMDB-1169 EMDB-5327 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Cell, Vol. 118, Issue 4, Page 465-75, Year 2004
Title	Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
Authors	Christian M T Spahn, Eric Jan, Anke Mulder, Robert A Grassucci, Peter Sarnow, Joachim Frank Howard Hughes Medical Institute, Health Research Inc. at, Albany, NY 10012, USA.
Keywords	Conserved Sequence, Cryoelectron Microscopy (methods), Escherichia coli (metabolism), HeLa Cells, Humans, Models, Molecular, Protein Binding, Protein Biosynthesis, Protein Conformation, RNA, Messenger (metabolism), RNA, Transfer (metabolism, 9014-25-9), RNA, Viral (metabolism), Ribosomes (chemistry)
Links	PubMed: 15315759, DOI: 10.1016/j.cell.2004.08.001, PII: S0092867404007469

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

float (32-bit)

Space Group Number

Map Geometry

Unit Cell

A= B= C: 457.5 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= Z: 3.66 A

CCP4 map header info

Annotation Details

map

Sample
Name	Human ribosome 80S bound with CrPV IRES
Number of Components	2
Component #1: ribosome-eukaryote - Human ribosome 80s
Scientific name	Human ribosome 80s
Scientific Name of Species	Homo sapiens
Common Name of Species	Human
NCBI taxonomy	9606
Eukaryote	ALL
Recombinant expression	No
Component #2: protein - CrPV IRES
Scientific name	CrPV IRES
Scientific Name of Species	Cricket paralysis virus
NCBI taxonomy	12136
Recombinant expression	No

Experiment
Sample Preparation
Specimen State	particle
Vitrification
Cryogen Name	ETHANE
Imaging
Microscope	FEI TECNAI F30
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	300 kV
Electron Dose	20 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 39000, Calibrated: 38000
Astigmatism	objective lens astigmatism was corrected at 100,000 times magnification
Imaging Mode	BRIGHT FIELD
Specimen Holder
Holder	FEI Polara cartridge system
Model	OTHER
Tilt Angle	0 degrees - 0 degrees
Temperature	K ( - 84 K)
Camera
Detector	Kodak SO163 film
Image Acquisition
Sampling Size	14
Scanner	ZEISS SCAI

Processing
Method	single particle reconstruction
3D reconstruction
Algorithm	Back projection
Software	SPIDER
CTF Correction	defocus group volumes
Resolution By Author	17.3 A
Resolution Method	FSC at 0.5 cut-off

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), 3.4 MB .webm (WebM/VP8 format), 5.2 MB Session file for UCSF-Chimera, 26.8 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.1 MB .webm (WebM/VP8 format), 4.5 MB Session file for UCSF-Chimera, 26.9 KB