› 7ea5

Electron Microscopy
3.3Å resolution

Yeast Set2 bound to a nucleosome containing oncohistone mutations

Released:
DOI: 10.2210/pdb7ea5/pdb
PDB entry 7ea5 coloured by chain, front view.
PDB entry 7ea5 coloured by chain, side view.
PDB entry 7ea5 coloured by chain, top view.
Source organisms:
Primary publication:
Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations.
Liu Y, Zhang Y, Xue H, Cao M, Bai G, Mu Z, Yao Y, Sun S, Fang D, Huang J
OpenAccess logo Cell Discov 7 32 (2021)
PMID: 33972509
Related structures: EMD-31039

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 undecamer (preferred)
PDBe Complex ID:
PDB-CPX-121236 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 101 amino acids
Theoretical weight: 11.85 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P84233 (Residues: 35-135; Coverage: 74%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 78 amino acids
Theoretical weight: 8.85 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 25-102; Coverage: 76%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A Chains: C, G
Molecule details ›
Chains: C, G
Length: 105 amino acids
Theoretical weight: 11.49 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6AZJ8 (Residues: 14-118; Coverage: 81%)
Gene names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
Sequence domains:
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 93 amino acids
Theoretical weight: 10.41 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P02281 (Residues: 32-124; Coverage: 74%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone-lysine N-methyltransferase, H3 lysine-36 specific Chain: K
Molecule details ›
Chain: K
Length: 228 amino acids
Theoretical weight: 26.7 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P46995 (Residues: 33-260; Coverage: 31%)
Gene names: EZL1, J0520, KMT3, SET2, YJL168C
Sequence domains:
601-DNA Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.52 KDa
601-DNA Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.99 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand SAM 1 x SAM
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-31039
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli
  • Escherichia coli BL21

Quick links

Citations

5 review citations

SETD2: from chromatin modifier to multipronged regulator of the genome and beyond.
Molenaar et al. (2022)
4 more

1 mention without citation

The engagement of histone lysine methyltransferases with nucleosomes: structural basis, regulatory mechanisms, and therapeutic implications.
Li et al. (2023)