› 3fdt

X-ray diffraction
2Å resolution

Crystal structure of the complex of human chromobox homolog 5 (CBX5) with H3K9(me)3 peptide

Released:
DOI: 10.2210/pdb3fdt/pdb
PDB entry 3fdt coloured by chain, front view.
PDB entry 3fdt coloured by chain, side view.
PDB entry 3fdt coloured by chain, top view.
Source organisms:
Primary publication:
Recognition and specificity determinants of the human cbx chromodomains.
Kaustov L, Ouyang H, Amaya M, Lemak A, Nady N, Duan S, Wasney GA, Li Z, Vedadi M, Schapira M, Min J, Arrowsmith CH
J Biol Chem 286 521-9 (2011)
PMID: 21047797

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-155376 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Chromobox protein homolog 5 Chain: A
Molecule details ›
Chain: A
Length: 59 amino acids
Theoretical weight: 7.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P45973 (Residues: 18-75; Coverage: 30%)
Gene names: CBX5, HP1A
Sequence domains: Chromo (CHRromatin Organisation MOdifier) domain
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Histone H3.1 Chain: T
Molecule details ›
Chain: T
Length: 15 amino acids
Theoretical weight: 1.61 KDa
Source organism: synthetic construct
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-16; Coverage: 11%)
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 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P41212
Unit cell:
a: 73.123Å b: 73.123Å c: 28.413Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.197 0.257
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

36 review citations

Roles of the Polycomb group proteins in stem cells and cancer.
Richly et al. (2011)
35 more

21 mentions without citation

Biomolecular Condensates in the Nucleus.
Sabari et al. (2020)
20 more