› 3qby

X-ray diffraction
1.95Å resolution

Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2

Released:
DOI: 10.2210/pdb3qby/pdb
PDB entry 3qby coloured by chain, front view.
PDB entry 3qby coloured by chain, side view.
PDB entry 3qby coloured by chain, top view.
Source organisms:
Primary publication:
Structural and histone binding ability characterizations of human PWWP domains.
Wu H, Zeng H, Lam R, Tempel W, Amaya MF, Xu C, Dombrovski L, Qiu W, Wang Y, Min J
PLoS One 6 e18919 (2011)
PMID: 21720545

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158682 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Hepatoma-derived growth factor-related protein 2 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q7Z4V5 (Residues: 1-93; Coverage: 14%)
Gene names: HDGF2, HDGFL2, HDGFRP2, HRP2, UNQ785/PRO1604
Sequence domains: PWWP domain
Structure domains: SH3 type barrels.
Histone H4 Chain: H
Molecule details ›
Chain: H
Length: 11 amino acids
Theoretical weight: 1.44 KDa
Source organism: synthetic construct
Expression system: Not provided
UniProt:
  • Canonical: P62805 (Residues: 16-26; Coverage: 11%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4

Ligands and Environments

2 bound ligands:
Ligand UNX 20 x UNX
Ligand SO4 2 x SO4
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P212121
Unit cell:
a: 41.527Å b: 41.681Å c: 156.749Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.216 0.253
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

28 review citations

Perceiving the epigenetic landscape through histone readers.
Musselman et al. (2012)
27 more

4 mentions without citation

PWWP domains and their modes of sensing DNA and histone methylated lysines.
Rona et al. (2016)
3 more