1B34

CRYSTAL STRUCTURE OF THE D1D2 SUB-COMPLEX FROM THE HUMAN SNRNP CORE DOMAIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs.

Kambach, C.Walke, S.Young, R.Avis, J.M.de la Fortelle, E.Raker, V.A.Luhrmann, R.Li, J.Nagai, K.

(1999) Cell 96: 375-387

  • DOI: https://doi.org/10.1016/s0092-8674(00)80550-4
  • Primary Citation of Related Structures:  
    1B34, 1D3B

  • PubMed Abstract: 

    The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F, and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs (snRNAs). These proteins share a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Crystal structures of two Sm protein complexes, D3B and D1D2, show that these proteins have a common fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta sheet, and the D1D2 and D3B dimers superpose closely in their core regions, including the dimer interfaces. The crystal structures suggest that the seven Sm proteins could form a closed ring and the snRNAs may be bound in the positively charged central hole.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, England, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1)119Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62314 (Homo sapiens)
Explore P62314 
Go to UniProtKB:  P62314
PHAROS:  P62314
GTEx:  ENSG00000167088 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62314
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D2)118Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62316 (Homo sapiens)
Explore P62316 
Go to UniProtKB:  P62316
PHAROS:  P62316
GTEx:  ENSG00000125743 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62316
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.249 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.3α = 90
b = 75.3β = 90
c = 91.99γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-01-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-12-07
    Changes: Database references
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references