Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.51 kDa 
• Atom Count: 3724 
• Modelled Residue Count: 440 
• Deposited Residue Count: 538 
• Unique protein chains: 2

3OMG

Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R14me2s

• DOI: 10.2210/pdb3OMG/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-26 Released: 2010-09-08 
• Deposition Author(s): Lam, R., Liu, K., Guo, Y.H., Bian, C.B., Xu, C., MacKenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.239 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain.

Liu, K., Chen, C., Guo, Y., Lam, R., Bian, C., Xu, C., Zhao, D.Y., Jin, J., MacKenzie, F., Pawson, T., Min, J.

(2010) Proc Natl Acad Sci U S A 107: 18398-18403

• PubMed: 20937909 
• DOI: 10.1073/pnas.1013106107
• Primary Citation of Related Structures:  
  3OMC, 3OMG


• PubMed Abstract: 
  

Arginine methylation modulates diverse cellular processes and represents a molecular signature of germ-line-specific Piwi family proteins. A subset of Tudor domains recognize arginine methylation modifications, but the binding mechanism has been lacking. Here we establish that, like other germ-line Tudor proteins, the ancestral staphylococcal nuclease domain-containing 1 (SND1) polypeptide is expressed and associates with PIWIL1/Miwi in germ cells. We find that human SND1 binds PIWIL1 in an arginine methylation-dependent manner with a preference for symmetrically dimethylated arginine. The entire Tudor domain and a bifurcated SN domain are required for this binding activity, whereas the canonical Tudor domain alone is insufficient for methylarginine ligand binding. Crystal structures show that the intact SND1 extended Tudor domain forms a wide and negatively charged binding groove, which can accommodate distinct symmetrically dimethylated arginine peptides from PIWIL1 in different orientations. This analysis explains how SND1 preferentially recognizes symmetrical dimethylarginine via an aromatic cage and conserved hydrogen bonds, and provides a general paradigm for the binding mechanisms of methylarginine-containing peptides by extended Tudor domains.

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Organizational Affiliation: 

Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Huazhong Normal University, Wuhan 430079, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal nuclease domain-containing protein 1	A, B	261	Homo sapiens	Mutation(s): 0  Gene Names: SND1, TDRD11 EC: 3.1.31.1
Find proteins for Q7KZF4 (Homo sapiens) Explore Q7KZF4  Go to UniProtKB:  Q7KZF4
NIH Common Fund Data Resources
PHAROS:  Q7KZF4 GTEx:  ENSG00000197157

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
dimethylated arginine peptide R14me2s	C, D	8	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2MR	C,D	L-PEPTIDE LINKING	C8 H18 N4 O2		ARG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.239 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.721	α = 90
b = 75.804	β = 90.36
c = 80.073	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-08-26 
• Released Date: 2010-09-08 
Deposition Author(s): Lam, R., Liu, K., Guo, Y.H., Bian, C.B., Xu, C., MacKenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description