1D3B

CRYSTAL STRUCTURE OF THE D3B SUBCOMPLEX OF THE HUMAN CORE SNRNP DOMAIN AT 2.0A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 

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

  • Primary Citation of Related Structures:  
  • Also Cited By: 4WZJ, 4V5U, 3CW1, 2Y9D, 2Y9C, 2Y9B, 2Y9A

  • 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 spliceosoma ...

    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.


    Related Citations: 
    • Structure and Assembly of the Spliceosomal Small Nuclear Ribonucleoprotein Particles
      Kambach, C.,Walke, S.,Nagai, K.
      (1999) Curr.Opin.Struct.Biol. 9: 222


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)
A, C, E, G, I, K
75Homo sapiensMutation(s): 1 
Gene Names: SNRPD3
Find proteins for P62318 (Homo sapiens)
Go to Gene View: SNRPD3
Go to UniProtKB:  P62318
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)
B, D, F, H, J, L
91Homo sapiensMutation(s): 0 
Gene Names: SNRPB (COD, SNRPB1)
Find proteins for P14678 (Homo sapiens)
Go to Gene View: SNRPB
Go to UniProtKB:  P14678
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
B, G, I
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 107.350α = 90.00
b = 108.450β = 90.00
c = 110.420γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SHARPphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-22
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2011-12-07
    Type: Database references
  • Version 1.4: 2018-03-14
    Type: Database references