1MHN

High resolution crystal structure of the SMN Tudor domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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


  • 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-termin ...

    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.


    Related Citations: 
    • Definition of domain boundaries and crystallization of the SMN Tudor domain
      Sprangers, R.,Selenko, P.,Sattler, M.,Sinning, I.,Groves, M.R.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Survival motor neuron protein
A
59Homo sapiensMutation(s): 0 
Gene Names: SMN1, SMN2 (SMN, SMNT, SMNC)
Find proteins for Q16637 (Homo sapiens)
Go to Gene View: SMN1 SMN2
Go to UniProtKB:  Q16637
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.144 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 27.652α = 90.00
b = 27.652β = 90.00
c = 110.299γ = 120.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
CNSphasing
SCALAdata scaling
REFMACrefinement
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance