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 1.5 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 D3)
A, C, E, G, I
A, C, E, G, I, K
75Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P62318 (Homo sapiens)
Explore P62318 
Go to UniProtKB:  P62318
PHAROS:  P62318
GTEx:  ENSG00000100028 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62318
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 ASSOCIATED PROTEIN B)
B, D, F, H, J
B, D, F, H, J, L
91Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P14678 (Homo sapiens)
Explore P14678 
Go to UniProtKB:  P14678
PHAROS:  P14678
GTEx:  ENSG00000125835 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14678
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / 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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth I]
CA [auth L]
M [auth A]
N [auth A]
P [auth B]
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
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

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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
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations