PDBe 4c1q

X-ray diffraction
2.3Å resolution

Crystal structure of the PRDM9 SET domain in complex with H3K4me2 and AdoHcy.

Released:

Function and Biology Details

Reaction catalysed:
S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase PRDM9 Chains: A, B
Molecule details ›
Chains: A, B
Length: 175 amino acids
Theoretical weight: 19.9 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96EQ9 (Residues: 198-368; Coverage: 20%)
Gene names: Hst1, Meisetz, Prdm9
Sequence domains: SET domain
Structure domains: SET domain
Histone H3.1 Chain: C
Molecule details ›
Chain: C
Length: 10 amino acids
Theoretical weight: 1.25 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-11; Coverage: 7%)
Gene names: H3FA, H3FB, H3FC, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P212121
Unit cell:
a: 55.73Å b: 78.18Å c: 107.61Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.252
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided