High resolution crystal structure of the SMN Tudor domain

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.147 

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High Resolution X-ray and NMR Structures of the SMN Tudor Domain: conformational variation in the binding site for symmetrically dimethylated arginine residues

Sprangers, R.Groves, M.R.Sinning, I.Sattler, M.

(2003) J Mol Biol 327: 507-520

  • DOI: https://doi.org/10.1016/s0022-2836(03)00148-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The SMN protein, which is linked to spinal muscular atrophy (SMA), plays an important role in the assembly of the spliceosomal small nuclear ribonucleoprotein complexes. This function requires binding of SMN to the arginine-glycine (RG) rich C-terminal tails of the Sm proteins, which contain symmetrically dimethylated arginine residues (sDMA) in vivo. Using NMR titrations, we show that the SMN Tudor domain recognizes these sDMAs in the methylated RG repeats. Upon complex formation a cluster of conserved aromatic residues in the SMN Tudor domain interacts with the sDMA methyl groups. We present two high resolution structures of the uncomplexed SMN Tudor domain, a 1.8A crystal structure and an NMR structure that has been refined against a large number of backbone and side-chain residual dipolar couplings. The backbone conformation of both structures is very similar, however, differences are observed for the cluster of conserved aromatic side-chains in the sDMA binding pocket. In order to validate these variations we introduce a novel application of residual dipolar couplings for aromatic rings. We show that structural information can be derived from aromatic ring residual dipolar couplings, even in the presence of internal motions such as ring flipping. These residual dipolar couplings and ring current shifts independently confirm that the SMN Tudor domain adopts two different conformations in the sDMA binding pocket. The observed structural variations may play a role for the recognition of sDMAs.

  • Organizational Affiliation

    Structural and Computational Biology Programme, EMBL Heidelberg, Meyerhofstr. 1, Germany. spranger@embl.de

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Survival motor neuron protein59Homo sapiensMutation(s): 0 
Gene Names: smn1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16637 (Homo sapiens)
Explore Q16637 
Go to UniProtKB:  Q16637
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16637
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.147 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.652α = 90
b = 27.652β = 90
c = 110.299γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references