› 5jhn

X-ray diffraction
1.67Å resolution

Structure of G9a SET-domain with Histone H3K9Ala mutant peptide and bound S-adenosylmethionine

Released:
DOI: 10.2210/pdb5jhn/pdb
PDB entry 5jhn coloured by chain, front view.
PDB entry 5jhn coloured by chain, side view.
PDB entry 5jhn coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
S-adenosyl methionine is necessary for inhibition of the methyltransferase G9a by the lysine 9 to methionine mutation on histone H3.
Jayaram H, Hoelper D, Jain SU, Cantone N, Lundgren SM, Poy F, Allis CD, Cummings R, Bellon S, Lewis PW
Proc Natl Acad Sci U S A 113 6182-7 (2016)
PMID: 27185940

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-L-lysine(9) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(9)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159461 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase EHMT2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 274 amino acids
Theoretical weight: 31.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96KQ7 (Residues: 916-1189; Coverage: 23%)
Gene names: BAT8, C6orf30, EHMT2, G9A, KMT1C, NG36
Sequence domains:
Structure domains: SET domain
Histone H3.1 Chains: F, G
Molecule details ›
Chains: F, G
Length: 11 amino acids
Theoretical weight: 1.08 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 4-14; Coverage: 8%)
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

2 bound ligands:
Ligand ZN 8 x ZN
Ligand SAM 2 x SAM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P21
Unit cell:
a: 56.782Å b: 78.27Å c: 73.121Å
α: 90° β: 90.34° γ: 90°
R-values:
R R work R free
0.21 0.209 0.237
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

17 review citations

PRC2 is high maintenance.
Yu et al. (2019)
16 more

3 mentions without citation

S-adenosyl methionine is necessary for inhibition of the methyltransferase G9a by the lysine 9 to methionine mutation on histone H3.
Jayaram et al. (2016)
2 more