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- EMDB-1847: Human 35S U5 snRNP -

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Basic information

Entry
Database: EMDB / ID: EMD-1847
TitleHuman 35S U5 snRNP
Map dataThis is a 3D map of the human 35S U5 snRNP
Sample
  • Sample: Human spliceosomal 35S U5 snRNP
  • Organelle or cellular component: Human spliceosomal 35S U5 snRNP
KeywordsSpliceosome / pre-mRNA splicing / 35S U5 snRNP
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 27.8 Å
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-
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: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1847.png

Downloads & links

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Map

FileDownload / File: emd_1847.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 3D map of the human 35S U5 snRNP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.1 Å/pix.
x 128 pix.
= 652.8 Å		5.1 Å/pix.
x 128 pix.
= 652.8 Å		5.1 Å/pix.
x 128 pix.
= 652.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.91831625 - 1.02373672
Average (Standard dev.)0.00172093 (±0.03743135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 652.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.15.15.1
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z652.800652.800652.800
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-0.9181.0240.002

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Supplemental data

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Sample components

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Entire : Human spliceosomal 35S U5 snRNP

EntireName: Human spliceosomal 35S U5 snRNP
Components
  • Sample: Human spliceosomal 35S U5 snRNP
  • Organelle or cellular component: Human spliceosomal 35S U5 snRNP

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Supramolecule #1000: Human spliceosomal 35S U5 snRNP

SupramoleculeName: Human spliceosomal 35S U5 snRNP / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 2.4 MDa

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Supramolecule #1: Human spliceosomal 35S U5 snRNP

SupramoleculeName: Human spliceosomal 35S U5 snRNP / type: organelle_or_cellular_component / ID: 1 / Name.synonym: 35S U5 snRNP / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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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 / 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 FIELD
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: 27.8 Å / Resolution method: FSC 0.5 CUT-OFF

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