› 4u68

X-ray diffraction
1.8Å resolution

Crystal structure of Rhino chromodomain in complex with H3K9me3

Released:
DOI: 10.2210/pdb4u68/pdb
PDB 4u68 coloured by chain and viewed from the front.
PDB 4u68 coloured by chain and viewed from the side.
PDB 4u68 coloured by chain and viewed from the top.
Source organisms:
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)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Chromo domain-containing protein 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, Dmel\CG10683, Dmel_CG10683, HP1, HP1D, HP1d, RHI, Rhi, Rhino, hp1d, rhi, rhino, rno
Sequence domains: Chromo (CHRromatin Organisation MOdifier) domain
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Histone H3.1 Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 11 amino acids
Theoretical weight: 1.21 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 5-15; Coverage: 8%)
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

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

4 review citations

PIWI-interacting RNAs: Mitochondria-based biogenesis and functions in cancer.
Su et al. (2021)
3 more

1 mention without citation

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