› 5t0m

X-ray diffraction
1.9Å resolution

A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading

Released:
DOI: 10.2210/pdb5t0m/pdb
PDB entry 5t0m coloured by chain, front view.
PDB entry 5t0m coloured by chain, side view.
PDB entry 5t0m coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading.
Shan CM, Wang J, Xu K, Chen H, Yue JX, Andrews S, Moresco JJ, Yates JR, Nagy PL, Tong L, Jia S
Elife 5 (2016)
PMID: 27648579

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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159436 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase EHMT2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 281 amino acids
Theoretical weight: 32.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96KQ7 (Residues: 913-1193; Coverage: 23%)
Gene names: BAT8, C6orf30, EHMT2, G9A, KMT1C, NG36
Sequence domains:
Structure domains: SET domain
Histone H3.1 Chains: C, P
Molecule details ›
Chains: C, P
Length: 15 amino acids
Theoretical weight: 1.55 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-16; Coverage: 11%)
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

3 bound ligands:
Ligand ZN 8 x ZN
Ligand SAM 2 x SAM
Ligand SAH 1 x SAH
1 modified residue:
Ligand NLE 2 x NLE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 56.623Å b: 78.284Å c: 71.803Å
α: 90° β: 91.16° γ: 90°
R-values:
R R work R free
0.186 0.184 0.224
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

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

2 mentions without citation

A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading.
Shan et al. (2016)
1 more