› 5t1i

X-ray diffraction
1.6Å resolution

CBX3 chromo shadow domain in complex with histone H3 peptide

Released:
DOI: 10.2210/pdb5t1i/pdb
PDB entry 5t1i coloured by chain, front view.
PDB entry 5t1i coloured by chain, side view.
PDB entry 5t1i coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1.
Liu Y, Qin S, Lei M, Tempel W, Zhang Y, Loppnau P, Li Y, Min J
J Biol Chem 292 5655-5664 (2017)
PMID: 28223359

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159404 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Chromobox protein homolog 3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 68 amino acids
Theoretical weight: 7.64 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13185 (Residues: 110-176; Coverage: 37%)
Gene name: CBX3
Sequence domains: Chromo shadow domain
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Histone H3.1 Chain: C
Molecule details ›
Chain: C
Length: 15 amino acids
Theoretical weight: 1.87 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 39-53; 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

1 bound ligand:
Ligand UNX 12 x UNX
1 modified residue:
Ligand AAR 1 x AAR

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 40.737Å b: 34.971Å c: 45.833Å
α: 90° β: 93.32° γ: 90°
R-values:
R R work R free
0.197 0.194 0.239
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Shining Light on the Dark Side of the Genome.
Wallrath et al. (2022)
1 more

2 mentions without citation

Heterochromatin protein 1 (HP1): interactions with itself and chromatin components.
Kumar et al. (2020)
1 more