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- EMDB-1043: Molecular architecture of the multiprotein splicing factor SF3b. -

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Basic information

Entry
Database: EMDB / ID: EMD-1043
TitleMolecular architecture of the multiprotein splicing factor SF3b.
Map data3D map of SF3b
Sample
  • Sample: SF3b, multiprotein splicing factor
  • Protein or peptide: splicing related proteins
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 9.7 Å
AuthorsGolas MM / Sander B / Will CL / Luhrmann R / Stark H
CitationJournal: Science / Year: 2003
Title: Molecular architecture of the multiprotein splicing factor SF3b.
Authors: Monika M Golas / Bjoern Sander / Cindy L Will / Reinhard Lührmann / Holger Stark /
Abstract: The splicing factor SF3b is a multiprotein complex essential for the accurate excision of introns from pre-messenger RNA. As an integral component of the U2 small nuclear ribonucleoprotein (snRNP) ...The splicing factor SF3b is a multiprotein complex essential for the accurate excision of introns from pre-messenger RNA. As an integral component of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP, SF3b is involved in the recognition of the pre-messenger RNA's branch site within the major and minor spliceosomes. We have determined the three-dimensional structure of the human SF3b complex by single-particle electron cryomicroscopy at a resolution of less than 10 angstroms, allowing identification of protein domains with known structural folds. The best fit of a modeled RNA-recognition motif indicates that the protein p14 is located in the central cavity of the complex. The 22 tandem helical repeats of the protein SF3b155 are located in the outer shell of the complex enclosing p14.
History
DepositionApr 7, 2003-
Header (metadata) releaseApr 9, 2003-
Map releaseApr 9, 2005-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.029823325
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.029823325
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1043.gif

Downloads & links

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Map

FileDownload / File: emd_1043.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of SF3b
Voxel sizeX=Y=Z: 1.6 Å
Density
Contour Level1: 0.0108 / Movie #1: 0.0298233
Minimum - Maximum-0.131495 - 0.238562
Average (Standard dev.)0.0000174963 (±0.016553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 204.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.61.61.6
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z204.800204.800204.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1310.2390.000

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Supplemental data

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Sample components

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Entire : SF3b, multiprotein splicing factor

EntireName: SF3b, multiprotein splicing factor
Components
  • Sample: SF3b, multiprotein splicing factor
  • Protein or peptide: splicing related proteins

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Supramolecule #1000: SF3b, multiprotein splicing factor

SupramoleculeName: SF3b, multiprotein splicing factor / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightExperimental: 445 KDa / Theoretical: 450 KDa / Method: protein sequences

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Macromolecule #1: splicing related proteins

MacromoleculeName: splicing related proteins / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: Hela / Organelle: Nucleus / Location in cell: Nucleus
Molecular weightExperimental: 450 KDa / Theoretical: 445 KDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.9
Details: 20 mM Hepes, 600 mM KCl, 1.5 mM Mg2 Cl2, 5% glycerol, 0.5 mM DTT, 0.5 mM PMSF
StainingType: NEGATIVE
Details: The SF3b complexes were sandwiched in 2% uranyl formate between two layers of thin carbon using a perforated carbon grid as support. After 2 min at RT, the sample was frozen in liquid nitrogen.
GridDetails: 200 mesh copper grid
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.15 µm / Nominal magnification: 50000
Sample stageSpecimen holder: side entry cryo holder / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 93 K
Alignment procedureLegacy - Astigmatism: 175,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 4 µm / Number real images: 37 / Average electron dose: 20 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Number images used: 31000
Detailsinteractively

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Atomic model buiding 1

SoftwareName: Situs, Amira
RefinementOverall B value: 28

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