› 3qj6

X-ray diffraction
2.3Å resolution

The crystal structure of PWWP domain of human Hepatoma-derived growth factor 2 in complex with H3K79me3 peptide

Released:
DOI: 10.2210/pdb3qj6/pdb
PDB entry 3qj6 coloured by chain, front view.
PDB entry 3qj6 coloured by chain, side view.
PDB entry 3qj6 coloured by chain, top view.
Source organism: Homo sapiens
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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159417 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Hepatoma-derived growth factor-related protein 2 Chain: A
Molecule details ›
Chain: A
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 H3.1 Chain: T
Molecule details ›
Chain: T
Length: 12 amino acids
Theoretical weight: 1.54 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 74-85; Coverage: 9%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P61
Unit cell:
a: 74.934Å b: 74.934Å c: 41.764Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.236 0.234 0.276
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

3 mentions without citation

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