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- EMDB-1257: Organization of core spliceosomal components U5 snRNA loop I and ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1257
TitleOrganization of core spliceosomal components U5 snRNA loop I and U4/U6 Di-snRNP within U4/U6.U5 Tri-snRNP as revealed by electron cryomicroscopy.
Map data3D map of human U4/U6.U5 tri-snRNP
Sample
  • Sample: Human U4U6.U5 tri-snRNP
  • Organelle or cellular component: Human U4U6.U5 tri-snRNP
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 24.0 Å
AuthorsSander B / Golas MM / Kastner B / Luhrmann R
CitationJournal: Mol Cell / Year: 2006
Title: Organization of core spliceosomal components U5 snRNA loop I and U4/U6 Di-snRNP within U4/U6.U5 Tri-snRNP as revealed by electron cryomicroscopy.
Authors: Bjoern Sander / Monika M Golas / Evgeny M Makarov / Hero Brahms / Berthold Kastner / Reinhard Lührmann / Holger Stark /
Abstract: In eukaryotes, pre-mRNA exons are interrupted by large noncoding introns. Alternative selection of exons and nucleotide-exact removal of introns are performed by the spliceosome, a highly dynamic ...In eukaryotes, pre-mRNA exons are interrupted by large noncoding introns. Alternative selection of exons and nucleotide-exact removal of introns are performed by the spliceosome, a highly dynamic macromolecular machine. U4/U6.U5 tri-snRNP is the largest and most conserved building block of the spliceosome. By 3D electron cryomicroscopy and labeling, the exon-aligning U5 snRNA loop I is localized at the center of the tetrahedrally shaped tri-snRNP reconstructed to approximately 2.1 nm resolution in vitrified ice. Independent 3D reconstructions of its subunits, U4/U6 and U5 snRNPs, show how U4/U6 and U5 combine to form tri-snRNP and, together with labeling experiments, indicate a close proximity of the spliceosomal core components U5 snRNA loop I and U4/U6 at the center of tri-snRNP. We suggest that this central tri-snRNP region may be the site to which the prespliceosomal U2 snRNA has to approach closely during formation of the catalytic core of the spliceosome.
History
DepositionAug 17, 2006-
Header (metadata) releaseAug 17, 2006-
Map releaseAug 17, 2008-
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: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1257.gif

Downloads & links

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Map

FileDownload / File: emd_1257.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of human U4/U6.U5 tri-snRNP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.69 Å/pix.
x 128 pix.
= 472.32 Å		3.69 Å/pix.
x 128 pix.
= 472.32 Å		3.69 Å/pix.
x 128 pix.
= 472.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.69 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0855 / Movie #1: 0.03
Minimum - Maximum-0.553362 - 2.0796
Average (Standard dev.)0.00290757 (±0.0567257)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 472.32 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.693.693.69
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z472.320472.320472.320
α/β/γ90.00090.00090.000
start NX/NY/NZ-60-60-60
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.5532.0800.003

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Supplemental data

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Sample components

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Entire : Human U4U6.U5 tri-snRNP

EntireName: Human U4U6.U5 tri-snRNP
Components
  • Sample: Human U4U6.U5 tri-snRNP
  • Organelle or cellular component: Human U4U6.U5 tri-snRNP

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Supramolecule #1000: Human U4U6.U5 tri-snRNP

SupramoleculeName: Human U4U6.U5 tri-snRNP / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human U4U6.U5 tri-snRNP

SupramoleculeName: Human U4U6.U5 tri-snRNP / type: organelle_or_cellular_component / ID: 1 / 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/ST
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF

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