› 5vc8

X-ray diffraction
1.8Å resolution

Crystal structure of the WHSC1 PWWP1 domain

Released:
DOI: 10.2210/pdb5vc8/pdb
PDB entry 5vc8 coloured by chain, front view.
PDB entry 5vc8 coloured by chain, side view.
PDB entry 5vc8 coloured by chain, top view.
Source organisms:
Primary publication:
Histone and DNA binding ability studies of the NSD subfamily of PWWP domains.
Zhang M, Yang Y, Zhou M, Dong A, Yan X, Loppnau P, Min J, Liu Y
Biochem Biophys Res Commun 569 199-206 (2021)
PMID: 34271259

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(36) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(36)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-509904 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Histone-lysine N-methyltransferase NSD2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 141 amino acids
Theoretical weight: 16.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O96028 (Residues: 211-350; Coverage: 10%)
Gene names: KIAA1090, MMSET, NSD2, TRX5, WHSC1
Sequence domains: PWWP domain
dodeca-2-deoxy-nucleotide, poorly resolved by electron density Chains: W, X, Y
Molecule details ›
Chains: W, X, Y
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*CP*TP*(DN))-3') Chain: Z
Molecule details ›
Chain: Z
Length: 3 nucleotides
Theoretical weight: 729 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand UNX 39 x UNX
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P43212
Unit cell:
a: 82.99Å b: 82.99Å c: 115.4Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.2 0.229
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

NSD family proteins: Rising stars as therapeutic targets.
He et al. (2024)
3 other articles

5 mentions without citation

Chemical and Biochemical Perspectives of Protein Lysine Methylation.
Luo M. (2018)
4 more