Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.14 kDa 
• Atom Count: 500 
• Modelled Residue Count: 64 
• Deposited Residue Count: 64 
• Unique protein chains: 1

4A4H

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

• PDB DOI: 10.2210/pdb4A4H/pdb
• BMRB: 18008

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-12 Released: 2011-11-30 
• Deposition Author(s): Tripsianes, K., Madl, T., Machyna, M., Fessas, D., Englbrecht, C., Fischer, U., Neugebauer, K.M., Sattler, M.

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Experimental Data Snapshot

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

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

• PubMed: 22101937 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SURVIVAL OF MOTOR NEURON-RELATED-SPLICING FACTOR 30	A	64	Homo sapiens	Mutation(s): 0  Gene Names: SMNDC1, SMNR, SPF30
UniProt & NIH Common Fund Data Resources
Find proteins for O75940 (Homo sapiens) Explore O75940  Go to UniProtKB:  O75940
PHAROS:  O75940 GTEx:  ENSG00000119953

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DA2	B [auth A]	NG,NG-DIMETHYL-L-ARGININE C8 H18 N4 O2 YDGMGEXADBMOMJ-LURJTMIESA-N

Binding Affinity Annotations
ID	Source	Binding 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

Entry History 

Deposition Data

• Deposited Date: 2011-10-12 
• Released Date: 2011-11-30 
Deposition Author(s): Tripsianes, K., Madl, T., Machyna, M., Fessas, D., Englbrecht, C., Fischer, U., Neugebauer, K.M., Sattler, M.

Revision History  

• 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