› 3omc

X-ray diffraction
1.77Å resolution

Structure of human SND1 extended tudor domain in complex with the symmetrically dimethylated arginine PIWIL1 peptide R4me2s

Released:
DOI: 10.2210/pdb3omc/pdb
PDB entry 3omc coloured by chain, front view.
PDB entry 3omc coloured by chain, side view.
PDB entry 3omc coloured by chain, top view.
Source organisms:
Primary publication:
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 DY, Jin J, MacKenzie F, Pawson T, Min J
Proc Natl Acad Sci U S A 107 18398-403 (2010)
PMID: 20937909

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-163862 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Staphylococcal nuclease domain-containing protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 261 amino acids
Theoretical weight: 29.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7KZF4 (Residues: 650-910; Coverage: 29%)
Gene names: SND1, TDRD11
Sequence domains:
Structure domains:
SYNTHETIC PEPTIDE Chains: C, D
Molecule details ›
Chains: C, D
Length: 8 amino acids
Theoretical weight: 888 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CL 1 x CL
1 modified residue:
Ligand 2MR 2 x 2MR

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 35.622Å b: 75.834Å c: 80.177Å
α: 90° β: 90.37° γ: 90°
R-values:
R R work R free
0.18 0.179 0.213
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

29 review citations

PIWI-interacting small RNAs: the vanguard of genome defence.
Siomi et al. (2011)
28 more

6 mentions without citation

Cellular consequences of arginine methylation.
Lorton et al. (2019)
5 more