› 6v3n

X-ray diffraction
2.7Å resolution

Crystal structure of CDYL2 in complex with H3K27me3

Released:
DOI: 10.2210/pdb6v3n/pdb
PDB entry 6v3n coloured by chain, front view.
PDB entry 6v3n coloured by chain, side view.
PDB entry 6v3n coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Basis for the Binding Selectivity of Human CDY Chromodomains.
Dong C, Liu Y, Lyu TJ, Beldar S, Lamb KN, Tempel W, Li Y, Li Z, James LI, Qin S, Wang Y, Min J
Cell Chem Biol 27 827-838.e7 (2020)
PMID: 32470319

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-159423 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Chromodomain Y-like protein 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 64 amino acids
Theoretical weight: 7.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8N8U2 (Residues: 2-64; Coverage: 13%)
Gene name: CDYL2
Sequence domains: Chromo (CHRromatin Organisation MOdifier) domain
Histone H3.1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 17 amino acids
Theoretical weight: 1.65 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 20-33; Coverage: 10%)
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 M3L 2 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P4322
Unit cell:
a: 60.792Å b: 60.792Å c: 178.6Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.241 0.24 0.258
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Chemical tools targeting readers of lysine methylation.
Ortiz et al. (2023)
2 other articles