› 5jlb

X-ray diffraction
1.5Å resolution

Crystal structure of SETD2 bound to histone H3.3 K36I peptide

Released:
DOI: 10.2210/pdb5jlb/pdb
PDB entry 5jlb coloured by chain, front view.
PDB entry 5jlb coloured by chain, side view.
PDB entry 5jlb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis for oncohistone H3 recognition by SETD2 methyltransferase.
Yang S, Zheng X, Lu C, Li GM, Allis CD, Li H
Genes Dev 30 1611-6 (2016)
PMID: 27474439

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(36) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(36)
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-160867 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase SETD2 Chain: A
Molecule details ›
Chain: A
Length: 279 amino acids
Theoretical weight: 32.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BYW2 (Residues: 1434-1711; Coverage: 11%)
Gene names: HIF1, HSPC069, HYPB, KIAA1732, KMT3A, SET2, SETD2
Sequence domains:
Histone H3.3 Chain: B
Molecule details ›
Chain: B
Length: 14 amino acids
Theoretical weight: 1.54 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P84243 (Residues: 30-43; Coverage: 10%)
Gene names: H3-3A, H3-3B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781

Ligands and Environments

4 bound ligands:
Ligand SAH 1 x SAH
Ligand SCN 3 x SCN
Ligand GOL 2 x GOL
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 60.593Å b: 76.844Å c: 77.264Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.164 0.19
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

35 review citations

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

4 mentions without citation

Molecular basis for oncohistone H3 recognition by SETD2 methyltransferase.
Yang et al. (2016)
3 more