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- EMDB-1594: 35-40S RNA editing complex of Trypanosoma brucei -

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Basic information

Entry
Database: EMDB / ID: EMD-1594
Title35-40S RNA editing complex of Trypanosoma brucei
Map data3D map of the 35-40S RNA editing complex of Trypanosoma brucei
Sample
  • Sample: 35-40S RNA editing complex
  • Organelle or cellular component: 35-40S RNA editing complex
KeywordsRNA editing / Trypanosoma brucei
Biological speciesTrypanosoma brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.0 Å
AuthorsGolas MM / Boehm C / Sander B / Effenberger K / Brecht M / Stark H / Goeringer HU
CitationJournal: EMBO J / Year: 2009
Title: Snapshots of the RNA editing machine in trypanosomes captured at different assembly stages in vivo.
Authors: Monika M Golas / Cordula Böhm / Bjoern Sander / Kerstin Effenberger / Michael Brecht / Holger Stark / H Ulrich Göringer /
Abstract: Mitochondrial pre-messenger RNAs in kinetoplastid protozoa are substrates of uridylate-specific RNA editing. RNA editing converts non-functional pre-mRNAs into translatable molecules and can generate ...Mitochondrial pre-messenger RNAs in kinetoplastid protozoa are substrates of uridylate-specific RNA editing. RNA editing converts non-functional pre-mRNAs into translatable molecules and can generate protein diversity by alternative editing. Although several editing complexes have been described, their structure and relationship is unknown. Here, we report the isolation of functionally active RNA editing complexes by a multistep purification procedure. We show that the endogenous isolates contain two subpopulations of approximately 20S and approximately 35-40S and present the three-dimensional structures of both complexes by electron microscopy. The approximately 35-40S complexes consist of a platform density packed against a semispherical element. The approximately 20S complexes are composed of two subdomains connected by an interface. The two particles are structurally related, and we show that RNA binding is a main determinant for the interconversion of the two complexes. The approximately 20S editosomes contain an RNA-binding site, which binds gRNA, pre-mRNA and gRNA/pre-mRNA hybrid molecules with nanomolar affinity. Variability analysis indicates that subsets of complexes lack or possess additional domains, suggesting binding sites for components. Together, a picture of the RNA editing machinery is provided.
History
DepositionJan 26, 2009-
Header (metadata) releaseFeb 25, 2009-
Map releaseJan 27, 2011-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1594.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of the 35-40S RNA editing complex of Trypanosoma brucei
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 160 pix.
= 432. Å
2.7 Å/pix.
x 160 pix.
= 432. Å
2.7 Å/pix.
x 160 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density
Contour LevelBy EMDB: 0.0419 / Movie #1: 0.0419
Minimum - Maximum-0.42813367 - 1.11607575
Average (Standard dev.)0.00226512 (±0.03254844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-17-17-200
NX/NY/NZ123123401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.4281.1160.002

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Supplemental data

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Sample components

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Entire : 35-40S RNA editing complex

EntireName: 35-40S RNA editing complex
Components
  • Sample: 35-40S RNA editing complex
  • Organelle or cellular component: 35-40S RNA editing complex

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Supramolecule #1000: 35-40S RNA editing complex

SupramoleculeName: 35-40S RNA editing complex / type: sample / ID: 1000 / Details: 1.45 +/- 0.15MDa / Number unique components: 1
Molecular weightExperimental: 1.45 MDa

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Supramolecule #1: 35-40S RNA editing complex

SupramoleculeName: 35-40S RNA editing complex / type: organelle_or_cellular_component / ID: 1 / Name.synonym: editosome / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Trypanosoma brucei (eukaryote) / synonym: trypanosome / Cell: Trypanosoma brucei / Organelle: mitochondrium

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: NITROGEN / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF

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