› 4gng

X-ray diffraction
1.73Å resolution

Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide

Released:
DOI: 10.2210/pdb4gng/pdb
PDB entry 4gng coloured by chain, front view.
PDB entry 4gng coloured by chain, side view.
PDB entry 4gng coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The methyltransferase NSD3 has chromatin-binding motifs, PHD5-C5HCH, that are distinct from other NSD (nuclear receptor SET domain) family members in their histone H3 recognition.
He C, Li F, Zhang J, Wu J, Shi Y
J Biol Chem 288 4692-703 (2013)
PMID: 23269674

Function and Biology Details

Reactions 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)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(27) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(27)
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-160868 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase NSD3 Chains: A, D
Molecule details ›
Chains: A, D
Length: 107 amino acids
Theoretical weight: 12.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9BZ95 (Residues: 1310-1413; Coverage: 7%)
Gene names: DC28, NSD3, WHSC1L1
Sequence domains: NSD Cys-His rich domain
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Histone H3.3 Chains: B, F
Molecule details ›
Chains: B, F
Length: 15 amino acids
Theoretical weight: 1.61 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P84243 (Residues: 2-16; Coverage: 11%)
Gene names: H3-3A, H3-3B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand GOL 3 x GOL
1 modified residue:
Ligand M3L 2 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 56.2Å b: 59.96Å c: 95.23Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.182 0.214
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

The Role of Nuclear Receptor-Binding SET Domain Family Histone Lysine Methyltransferases in Cancer.
Bennett et al. (2017)
8 more

1 mention without citation

The methyltransferase NSD3 has chromatin-binding motifs, PHD5-C5HCH, that are distinct from other NSD (nuclear receptor SET domain) family members in their histone H3 recognition.
He et al. (2013)