Solution structure of SMN Tudor domain in complex with symmetrically dimethylated arginine

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: LOWEST ENERGY 

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This is version 1.3 of the entry. See complete history


Structural Basis for Dimethyl-Arginine Recognition by the Tudor Domains of Human Smn and Spf30 Proteins

Tripsianes, K.Madl, T.Machyna, M.Fessas, D.Englbrecht, C.Fischer, U.Neugebauer, K.M.Sattler, M.

(2011) Nat Struct Mol Biol 18: 1414

  • DOI: https://doi.org/10.1038/nsmb.2185
  • Primary Citation of Related Structures:  
    4A4E, 4A4F, 4A4G, 4A4H

  • PubMed Abstract: 

    Arginine dimethylation plays critical roles in the assembly of ribonucleoprotein complexes in pre-mRNA splicing and piRNA pathways. We report solution structures of SMN and SPF30 Tudor domains bound to symmetric and asymmetric dimethylated arginine (DMA) that is inherent in the RNP complexes. An aromatic cage in the Tudor domain mediates dimethylarginine recognition by electrostatic stabilization through cation-π interactions. Distinct from extended Tudor domains, dimethylarginine binding by the SMN and SPF30 Tudor domains is independent of proximal residues in the ligand. Yet, enhanced micromolar affinities are obtained by external cooperativity when multiple methylation marks are presented in arginine- and glycine-rich peptide ligands. A hydrogen bond network in the SMN Tudor domain, including Glu134 and a tyrosine hydroxyl of the aromatic cage, enhances cation-π interactions and is impaired by a mutation causing an E134K substitution associated with spinal muscular atrophy. Our structural analysis enables the design of an optimized binding pocket and the prediction of DMA binding properties of Tudor domains.

  • Organizational Affiliation

    Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SURVIVAL MOTOR NEURON PROTEIN64Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16637 (Homo sapiens)
Explore Q16637 
Go to UniProtKB:  Q16637
PHAROS:  Q16637
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16637
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 2MR

Download Ideal Coordinates CCD File 
C8 H18 N4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
2MR PDBBind:  4A4E Kd: 4.76e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: LOWEST ENERGY 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2011-12-14
    Changes: Database references
  • Version 1.2: 2011-12-28
    Changes: Other
  • Version 1.3: 2023-06-14
    Changes: Data collection, Database references, Derived calculations, Other