› 3n71

X-ray diffraction
2.3Å resolution

Crystal structure of cardiac specific histone methyltransferase SmyD1

Released:
DOI: 10.2210/pdb3n71/pdb
PDB entry 3n71 coloured by chain, front view.
PDB entry 3n71 coloured by chain, side view.
PDB entry 3n71 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Crystal structure of cardiac-specific histone methyltransferase SmyD1 reveals unusual active site architecture.
Sirinupong N, Brunzelle J, Ye J, Pirzada A, Nico L, Yang Z
J Biol Chem 285 40635-44 (2010)
PMID: 20943667

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161304 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone-lysine N-methyltransferase Smyd1 Chain: A
Molecule details ›
Chain: A
Length: 490 amino acids
Theoretical weight: 56.58 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P97443 (Residues: 1-490; Coverage: 100%)
Gene names: Bop, Smyd1
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand SFG 1 x SFG
Ligand MES 1 x MES
Ligand GOL 2 x GOL
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: R3
Unit cell:
a: 170.5Å b: 170.5Å c: 57.1Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.209 0.209 0.256
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

14 review citations

Targeting histone lysine methylation in cancer.
McGrath et al. (2015)
13 more

11 mentions without citation

Structure and function of SET and MYND domain-containing proteins.
Spellmon et al. (2015)
10 more