› 3r93

X-ray diffraction
2.06Å resolution

Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3 peptide

Released:
DOI: 10.2210/pdb3r93/pdb
PDB entry 3r93 coloured by chain, front view.
PDB entry 3r93 coloured by chain, side view.
PDB entry 3r93 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for specific binding of human MPP8 chromodomain to histone H3 methylated at lysine 9.
Li J, Li Z, Ruan J, Xu C, Tong Y, Pan PW, Tempel W, Crombet L, Min J, Zang J
PLoS One 6 e25104 (2011)
PMID: 22022377

Function and Biology Details

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-180741 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
M-phase phosphoprotein 8 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 62 amino acids
Theoretical weight: 7.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99549 (Residues: 55-116; Coverage: 7%)
Gene names: MPHOSPH8, MPP8
Sequence domains: Chromo (CHRromatin Organisation MOdifier) domain
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Histone H3.2 Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 15 amino acids
Theoretical weight: 1.61 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q71DI3 (Residues: 2-16; Coverage: 11%)
Gene names: H3C13, H3C14, H3C15, H3F2, H3FM, HIST2H3A, HIST2H3C, HIST2H3D

Ligands and Environments

1 bound ligand:
Ligand UNX 3 x UNX
1 modified residue:
Ligand M3L 4 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21212
Unit cell:
a: 71.148Å b: 74.005Å c: 72.609Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.22 0.273
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Epigenetic regulation of epithelial-mesenchymal transition.
Sun et al. (2016)
6 more

7 mentions without citation

Crystal structure of the human SUV39H1 chromodomain and its recognition of histone H3K9me2/3.
Wang et al. (2012)
6 more