› 6bhe

X-ray diffraction
1.35Å resolution

Crystal structure of SETDB1 with a modified H3 peptide

Released:
DOI: 10.2210/pdb6bhe/pdb
PDB entry 6bhe coloured by chain, front view.
PDB entry 6bhe coloured by chain, side view.
PDB entry 6bhe coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1.
Jurkowska RZ, Qin S, Kungulovski G, Tempel W, Liu Y, Bashtrykov P, Stiefelmaier J, Jurkowski TP, Kudithipudi S, Weirich S, Tamas R, Wu H, Dombrovski L, Loppnau P, Reinhardt R, Min J, Jeltsch A
Nat Commun 8 2057 (2017)
PMID: 29234025

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) = S-adenosyl-L-homocysteine + a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(9)
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-159407 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase SETDB1 Chain: A
Molecule details ›
Chain: A
Length: 239 amino acids
Theoretical weight: 27.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q15047 (Residues: 190-410; Coverage: 17%)
Gene names: ESET, KIAA0067, KMT1E, SETDB1
Sequence domains:
Structure domains: SH3 type barrels.
Histone H3.1 Chain: B
Molecule details ›
Chain: B
Length: 18 amino acids
Theoretical weight: 1.86 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 4-20; Coverage: 13%)
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 36 x UNX
2 modified residues:
Ligand M3L 1 x M3L
Ligand ALY 1 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 37.051Å b: 71.372Å c: 52.055Å
α: 90° β: 104.23° γ: 90°
R-values:
R R work R free
0.136 0.134 0.172
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

15 review citations

Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials.
Cheng et al. (2019)
14 more

2 mentions without citation

H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1.
Jurkowska et al. (2017)
1 more