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- EMDB-1848: High salt resistant human spliceosomal C complex core -

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Basic information

Entry
Database: EMDB / ID: EMD-1848
TitleHigh salt resistant human spliceosomal C complex core
Map dataThis is a 3D map of the high-salt resistant human spliceosomal C complex core
Sample
  • Sample: High salt resistant human spliceosomal C complex core
  • Organelle or cellular component: High salt resistant human spliceosomal C complex core
Keywordsspliceosome / pre-mRNA splicing / C complex / high salt / core
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction
AuthorsGolas MM / Sander B / Bessonov S / Grote M / Wolf E / Kastner B / Stark H / Luhrmann R
CitationJournal: Mol Cell / Year: 2010
Title: 3D cryo-EM structure of an active step I spliceosome and localization of its catalytic core.
Authors: Monika M Golas / Bjoern Sander / Sergey Bessonov / Michael Grote / Elmar Wolf / Berthold Kastner / Holger Stark / Reinhard Lührmann /
Abstract: The spliceosome excises introns from pre-mRNA in a two-step splicing reaction. So far, the three-dimensional (3D) structure of a spliceosome with preserved catalytic activity has remained elusive. ...The spliceosome excises introns from pre-mRNA in a two-step splicing reaction. So far, the three-dimensional (3D) structure of a spliceosome with preserved catalytic activity has remained elusive. Here, we determined the 3D structure of the human, catalytically active step I spliceosome (C complex) by cryo-electron microscopy (cryo-EM) in vitrified ice. Via immunolabeling we mapped the position of the 5' exon. The C complex contains an unusually salt-stable ribonucleoprotein (RNP) core that harbors its catalytic center. We determined the 3D structure of this RNP core and also that of a post-step II particle, the 35S U5 snRNP, which contains most of the C complex core proteins. As C complex domains could be recognized in these structures, their position in the C complex could be determined, thereby allowing the region harboring the spliceosome's catalytic core to be localized.
History
DepositionDec 11, 2010-
Header (metadata) releaseMar 15, 2012-
Map releaseMar 15, 2012-
UpdateMar 15, 2012-
Current statusMar 15, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

image1848.png

Downloads & links

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Map

FileDownload / File: emd_1848.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 3D map of the high-salt resistant human spliceosomal C complex core
Voxel sizeX=Y=Z: 5.2 Å
Density
Contour LevelBy AUTHOR: 0.023 / Movie #1: 0.023
Minimum - Maximum-0.10940472 - 0.27262318
Average (Standard dev.)0.00096079 (±0.01142309)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 665.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.25.25.2
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z665.600665.600665.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-24-70
NX/NY/NZ6149141
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1090.2730.001

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Supplemental data

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Sample components

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Entire : High salt resistant human spliceosomal C complex core

EntireName: High salt resistant human spliceosomal C complex core
Components
  • Sample: High salt resistant human spliceosomal C complex core
  • Organelle or cellular component: High salt resistant human spliceosomal C complex core

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Supramolecule #1000: High salt resistant human spliceosomal C complex core

SupramoleculeName: High salt resistant human spliceosomal C complex core / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: High salt resistant human spliceosomal C complex core

SupramoleculeName: High salt resistant human spliceosomal C complex core / type: organelle_or_cellular_component / ID: 1 / Name.synonym: High salt core of spliceosomal C complex / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric)

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