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: 2.00 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

  • DOI: 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) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3)A, C, E, G, I, K75Homo sapiensMutation(s): 1 
Gene Names: SNRPD3
UniProt & NIH Common Fund Data Resources
Find proteins for P62318 (Homo sapiens)
Explore P62318 
Go to UniProtKB:  P62318
PHAROS:  P62318
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN B)B, D, F, H, J, L91Homo sapiensMutation(s): 0 
Gene Names: SNRPBCODSNRPB1
UniProt & NIH Common Fund Data Resources
Find proteins for P14678 (Homo sapiens)
Explore P14678 
Go to UniProtKB:  P14678
PHAROS:  P14678
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
AA [auth I], O [auth B], X [auth G]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth I] , CA [auth L] , M [auth A] , N [auth A] , P [auth B] , Q [auth B] , R [auth C] , S [auth D] , 
BA [auth I],  CA [auth L],  M [auth A],  N [auth A],  P [auth B],  Q [auth B],  R [auth C],  S [auth D],  T [auth E],  U [auth F],  V [auth F],  W [auth F],  Y [auth G],  Z [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.35α = 90
b = 108.45β = 90
c = 110.42γ = 90
Software Package:
Software NamePurpose
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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