› 4ijd

X-ray diffraction
2.15Å resolution

Crystal structure of methyltransferase domain of human PR domain-containing protein 9

Released:
DOI: 10.2210/pdb4ijd/pdb
PDB entry 4ijd coloured by chain, front view.
PDB entry 4ijd coloured by chain, side view.
PDB entry 4ijd coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Dong A, Dombrovski L, Li Y, Tempel W, Bountra C, Arrowsmith CH, Edwards AM, Brown PJ, Wu H, Structural Genomics Consortium (SGC)

Function and Biology Details

Reactions catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(9) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(9)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(36) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(36)
S-adenosyl-L-methionine + a [histone H4]-L-lysine(20) = S-adenosyl-L-homocysteine + a [histone H4]-N(6)-methyl-L-lysine(20)
S-adenosyl-L-methionine + a [histone H4]-N(6)-methyl-L-lysine(20) = S-adenosyl-L-homocysteine + a [histone H4]-N(6),N(6)-dimethyl-L-lysine(20)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192517 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone-lysine N-methyltransferase PRDM9 Chains: A, B
Molecule details ›
Chains: A, B
Length: 221 amino acids
Theoretical weight: 25.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9NQV7 (Residues: 195-415; Coverage: 25%)
Gene names: PFM6, PRDM9
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand UNX 24 x UNX
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 54.734Å b: 48.782Å c: 78.713Å
α: 90° β: 100.05° γ: 90°
R-values:
R R work R free
0.199 0.196 0.264
Expression system: Escherichia coli BL21

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