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20S RNA editing complex of Trypanosoma brucei

by single particle reconstruction, at 22 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0419, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.0419, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1595
Title20S RNA editing complex of Trypanosoma brucei
Map3D map of the 20S RNA editing complex of Trypanosoma brucei
Sample20S RNA editing complex of Trypanosoma bucei
KeywordsRNA editing, Trypanosoma brucei
AuthorsGolas MM, Boehm C, Sander B, Effenberger K, Brecht M, Stark H, Goeringer HU
DateDeposition: 2009-01-26, Header release: 2009-02-25, Map release: 2011-01-27, Last update: 2013-12-11
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0419, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.0419, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleEMBO J., Vol. 28, Issue 6, Page 766-78, Year 2009
TitleSnapshots of the RNA editing machine in trypanosomes captured at different assembly stages in vivo.
AuthorsMonika M Golas, Cordula Böhm, Bjoern Sander, Kerstin Effenberger, Michael Brecht, Holger Stark, H Ulrich Göringer
Research Group of 3D Electron Cryomicroscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
KeywordsAnimals, Cryoelectron Microscopy, Models, Biological, Models, Molecular, Protozoan Proteins (chemistry), RNA Editing, RNA, Protozoan (chemistry), Trypanosoma (metabolism), Ultracentrifugation
LinksDOI: 10.1038/emboj.2009.19, PubMed: 19197238, PMC: PMC2666021
Map
Fileemd_1595.map.gz ( map file in CCP4 format, 1025 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
5.7 A/pix
= 364.8 A
64 pix
5.7 A/pix
= 364.8 A
64 pix
5.7 A/pix
= 364.8 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.0419 (by emdb), 0.0419 (movie #1):
Minimum - Maximum: -0.65175891 - 1.61760938
Average (Standard dev.): 0.00520643 (0.06710754)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
Unit CellA= B= C: 364.8 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 5.7 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z5.75.75.7
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z364.800364.800364.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-75-75-74
NX/NY/NZ150150150
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.6521.6180.005
Annotation Details3D map of the 20S RNA editing complex of Trypanosoma brucei
Supplement
Images
Images
Sample
Name20S RNA editing complex of Trypanosoma bucei
Number of Components1
Details0.8 +/- 0.08MDa
Experimental Mass0.8MDa
Component #1: cellular-component - editosome
Scientific name20S RNA editing complex
Common Nameeditosome
Oligomeric Detailsmonomer
Scientific Name of SpeciesTrypanosoma brucei

Common Name of Speciestrypanosome
NCBI taxonomy5691
Recombinant expressionNo
Natural SourceOrganelle: mitochondria
Cell: Trypanosoma brucei
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameNITROGEN
InstrumentNONE
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage160 kV
Illumination ModeSPOT SCAN
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
Holdereucentric
ModelGATAN LIQUID NITROGEN
Camera
Processing
Methodsingle particle reconstruction
3D reconstruction
Resolution By Author22 A
Resolution MethodFSC 0.5
Single Particle
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1595.xml (5.6 KB)
Map dataemd_1595.map.gz (949.3 KB)
Imagesemd-1595.jpg (45 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1595
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 27.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 27.5 KB