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- EMDB-1066: Three-dimensional structure of a pre-catalytic human spliceosomal... -

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Basic information

Entry
Database: EMDB / ID: EMD-1066
TitleThree-dimensional structure of a pre-catalytic human spliceosomal complex B.
Map data3D map of the spliceosome (B delta U1)
Sample
  • Sample: HeLa human pre-catalytic Spliceosome, B delta U1
  • Organelle or cellular component: spliceosome
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 40.0 Å
AuthorsBoehringer D / Makarov EM / Sander B / Makarova OV / Kastner B / Luehrmann R / Stark H
CitationJournal: Nat Struct Mol Biol / Year: 2004
Title: Three-dimensional structure of a pre-catalytic human spliceosomal complex B.
Authors: Daniel Boehringer / Evgeny M Makarov / Bjoern Sander / Olga V Makarova / Berthold Kastner / Reinhard Lührmann / Holger Stark /
Abstract: Major structural changes occur in the spliceosome during its transition from the fully assembled complex B to the catalytically activated spliceosome. To understand the rearrangement, it is necessary ...Major structural changes occur in the spliceosome during its transition from the fully assembled complex B to the catalytically activated spliceosome. To understand the rearrangement, it is necessary to know the detailed three-dimensional structures of these complexes. Here, we have immunoaffinity-purified human spliceosomes (designated B Delta U1) at a stage after U4/U6.U5 tri-snRNP integration but before activation, and have determined the three-dimensional structure of B Delta U1 by single-particle electron cryomicroscopy at a resolution of approximately 40 A. The overall size of the complex is about 370 x 270 x 170 A. The three-dimensional structure features a roughly triangular body linked to a head domain in variable orientations. The body is very similar in size and shape to the isolated U4/U6.U5 tri-snRNP. This provides initial insight into the structural organization of complex B.
History
DepositionDec 23, 2003-
Header (metadata) releaseDec 23, 2003-
Map releaseDec 23, 2004-
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: 0.134651394
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.134651394
  • 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_1066.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of the spliceosome (B delta U1)
Voxel sizeX=Y=Z: 8.66 Å
Density
Contour Level1: 0.138 / Movie #1: 0.1346514
Minimum - Maximum-0.720368 - 0.958293
Average (Standard dev.)0.000000000029852 (±0.0917209)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 554.24 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.668.668.66
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z554.240554.240554.240
α/β/γ90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.7200.9580.000

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Supplemental data

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Sample components

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Entire : HeLa human pre-catalytic Spliceosome, B delta U1

EntireName: HeLa human pre-catalytic Spliceosome, B delta U1
Components
  • Sample: HeLa human pre-catalytic Spliceosome, B delta U1
  • Organelle or cellular component: spliceosome

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Supramolecule #1000: HeLa human pre-catalytic Spliceosome, B delta U1

SupramoleculeName: HeLa human pre-catalytic Spliceosome, B delta U1 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: spliceosome

SupramoleculeName: spliceosome / type: organelle_or_cellular_component / ID: 1 / Name.synonym: ribo nucleo protein complex / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: HeLa

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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: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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: 40.0 Å / Resolution method: OTHER

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