› 4u68

X-ray diffraction
1.8Å resolution

Crystal structure of Rhino chromodomain in complex with H3K9me3

Released:
DOI: 10.2210/pdb4u68/pdb
PDB entry 4u68 coloured by chain, front view.
PDB entry 4u68 coloured by chain, side view.
PDB entry 4u68 coloured by chain, top view.
Source organism: Drosophila melanogaster
Primary publication:
Structural insights into Rhino-mediated germline piRNA cluster formation.
Yu B, Cassani M, Wang M, Liu M, Ma J, Li G, Zhang Z, Huang Y
Cell Res 25 525-8 (2015)
PMID: 25613572

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-221664 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Chromo domain-containing protein rhino Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 75 amino acids
Theoretical weight: 8.44 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7JXA8 (Residues: 20-90; Coverage: 17%)
Gene names: CG10683, HP1, HP1D, rhi, rhino
Sequence domains: Chromo (CHRromatin Organisation MOdifier) domain
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Histone H3 Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 11 amino acids
Theoretical weight: 1.21 KDa
Source organism: Drosophila melanogaster
Expression system: Not provided
UniProt:
  • Canonical: P02299 (Residues: 5-15; Coverage: 8%)
Gene names: CG31613, CG33803, CG33806, CG33809, CG33812, CG33815, CG33818, CG33821, CG33824, CG33827, CG33830, CG33833, CG33836, CG33839, CG33842, CG33845, CG33848, CG33851, CG33854, CG33857, CG33860, CG33863, CG33866, His3, His3:CG31613, His3:CG33803, His3:CG33806, His3:CG33809, His3:CG33812, His3:CG33815, His3:CG33818, His3:CG33821, His3:CG33824, His3:CG33827, His3:CG33830, His3:CG33833, His3:CG33836, His3:CG33839, His3:CG33842, His3:CG33845, His3:CG33848, His3:CG33851, His3:CG33854, His3:CG33857, His3:CG33860, His3:CG33863, His3:CG33866

Ligands and Environments

No bound ligands
1 modified residue:
Ligand M3L 3 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2
Unit cell:
a: 50.946Å b: 67.679Å c: 79.75Å
α: 90° β: 106.46° γ: 90°
R-values:
R R work R free
0.186 0.184 0.206
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

piRNA Biogenesis in Drosophila melanogaster.
Huang et al. (2017)
4 more

1 mention without citation

Structural insights into Rhino-mediated germline piRNA cluster formation.
Yu et al. (2015)