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- EMDB-1595: 20S RNA editing complex of Trypanosoma brucei -

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Basic information

Entry
Database: EMDB / ID: 1595
Title20S RNA editing complex of Trypanosoma brucei
KeywordsRNA editing / Trypanosoma brucei
Sample20S RNA editing complex of Trypanosoma bucei
SourceTrypanosoma brucei / eukaryote / trypanosome /
Map data3D map of the 20S RNA editing complex of Trypanosoma brucei
Methodsingle particle reconstruction, at 22 A resolution
AuthorsGolas MM / Boehm C / Sander B / Effenberger K / Brecht M / Stark H / Goeringer HU
CitationEMBO J., 2009, 28, 766-778

EMBO J., 2009, 28, 766-778 StrPapers
Snapshots of the RNA editing machine in trypanosomes captured at different assembly stages in vivo.
Monika M Golas / Cordula Böhm / Bjoern Sander / Kerstin Effenberger / Michael Brecht / Holger Stark / H Ulrich Göringer

DateDeposition: Jan 26, 2009 / Header (metadata) release: Feb 25, 2009 / Map release: Jan 27, 2011 / Last update: Jan 26, 2009

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0419
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0419
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Slabnear <=> far

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Supplemental images

Downloads & links

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Map

Fileemd_1595.map.gz (map file in CCP4 format, 1025 KB)
Projections & slices

Image control

Size
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Others
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.

Voxel sizeX=Y=Z: 5.7 A
Density
Contour Level:0.0419 (by emdb), 0.0419 (movie #1):
Minimum - Maximum-0.65175891 - 1.61760938
Average (Standard dev.)0.00520643 (0.06710754)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
CellA=B=C: 364.8 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.6521.6180.005

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Supplemental data

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Sample components

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Entire 20S RNA editing complex of Trypanosoma bucei

EntireName: 20S RNA editing complex of Trypanosoma bucei / Details: 0.8 +/- 0.08MDa / Number of components: 1
MassExperimental: 800 kDa

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Component #1: cellular-component, 20S RNA editing complex

Cellular-componentName: 20S RNA editing complex / a.k.a: editosome / Oligomeric Details: monomer / Recombinant expression: No
SourceSpecies: Trypanosoma brucei / eukaryote / trypanosome /
Source (natural)Organelle: mitochondria / Cell: Trypanosoma brucei

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Experimental details

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Sample preparation

Specimen stateparticle
VitrificationInstrument: NONE / Cryogen name: NITROGEN

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: eucentric / Model: GATAN LIQUID NITROGEN

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
3D reconstructionResolution: 22 A / Resolution method: FSC 0.5

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