4A4H

Solution structure of SPF30 Tudor domain in complex with asymmetrically dimethylated arginine


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1038/nsmb.2185
  • Primary Citation of Related Structures:  

  • 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 ( ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SURVIVAL OF MOTOR NEURON-RELATED-SPLICING FACTOR 30
A
64Homo sapiensMutation(s): 0 
Gene Names: SMNDC1 (SMNR, SPF30)
Find proteins for O75940 (Homo sapiens)
Go to Gene View: SMNDC1
Go to UniProtKB:  O75940
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DA2
Query on DA2

Download SDF File 
Download CCD File 
A
NG,NG-DIMETHYL-L-ARGININE
ADMA
C8 H18 N4 O2
YDGMGEXADBMOMJ-LURJTMIESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DA2Kd: 1706000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: LOWEST ENERGY 
  • Olderado: 4A4H Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2011-12-14
    Type: Database references
  • Version 1.2: 2011-12-28
    Type: Other
  • Version 1.3: 2013-11-06
    Type: Atomic model, Derived calculations