5egb

X-ray diffraction
1.98Å resolution

Human PRDM9 allele-A ZnF Domain with Associated Recombination Hotspot DNA Sequence II

Released:
Source organism: Homo sapiens
Primary publication:
Structural basis for human PRDM9 action at recombination hot spots.
Genes Dev 30 257-65 (2016)
PMID: 26833727

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-118631 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Histone-lysine N-methyltransferase PRDM9 Chain: A
Molecule details ›
Chain: A
Length: 144 amino acids
Theoretical weight: 16.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NQV7 (Residues: 717-858; Coverage: 16%)
Gene names: PFM6, PRDM9
Sequence domains: Zinc finger, C2H2 type
DNA (5'-D(*AP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 21 nucleotides
Theoretical weight: 6.49 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*TP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 21 nucleotides
Theoretical weight: 6.4 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 34.575Å b: 79.221Å c: 68.415Å
α: 90° β: 95.42° γ: 90°
R-values:
R R work R free
0.194 0.192 0.22
Expression systems:
  • Escherichia coli
  • Not provided