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:  
    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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SURVIVAL OF MOTOR NEURON-RELATED-SPLICING FACTOR 30A64Homo sapiensMutation(s): 0 
Gene Names: SMNDC1SMNRSPF30
UniProt & NIH Common Fund Data Resources
Find proteins for O75940 (Homo sapiens)
Explore O75940 
Go to UniProtKB:  O75940
PHAROS:  O75940
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DA2 (Subject of Investigation/LOI)
Query on DA2

Download Ideal Coordinates CCD File 
B [auth A]NG,NG-DIMETHYL-L-ARGININE
C8 H18 N4 O2
YDGMGEXADBMOMJ-LURJTMIESA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DA2 PDBBind:  4A4H Kd: 1.71e+6 (nM) from 1 assay(s)
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




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: 2013-11-06
    Changes: Atomic model, Derived calculations