› 7ea8

Electron Microscopy
3.1Å resolution

Human SETD2 bound to a nucleosome containing oncohistone mutations

Released:
DOI: 10.2210/pdb7ea8/pdb
PDB entry 7ea8 coloured by chain, front view.
PDB entry 7ea8 coloured by chain, side view.
PDB entry 7ea8 coloured by chain, top view.
Source organism: Homo sapiens
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-31040

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:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-121237 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
Histone-lysine N-methyltransferase SETD2 Chain: L
Molecule details ›
Chain: L
Length: 245 amino acids
Theoretical weight: 28.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BYW2 (Residues: 1452-1696; Coverage: 10%)
Gene names: HIF1, HSPC069, HYPB, KIAA1732, KMT3A, SET2, SETD2
Sequence domains:
Histone H3.3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 101 amino acids
Theoretical weight: 11.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6PI79 (Residues: 34-134; 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: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62799 (Residues: 25-102; Coverage: 76%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1-D Chains: C, G
Molecule details ›
Chains: C, G
Length: 104 amino acids
Theoretical weight: 11.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P20671 (Residues: 15-118; Coverage: 80%)
Gene names: H2AC7, H2AFG, HIST1H2AD
Sequence domains:
Histone H2B type 1-J Chains: D, H
Molecule details ›
Chains: D, H
Length: 125 amino acids
Theoretical weight: 13.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06899 (Residues: 2-126; Coverage: 99%)
Gene names: H2BC11, H2BFR, HIST1H2BJ
Sequence domains: Core histone H2A/H2B/H3/H4
601-DNA Chain: I
Molecule details ›
Chain: I
Length: 122 nucleotides
Theoretical weight: 37.44 KDa
601-DNA Chain: J
Molecule details ›
Chain: J
Length: 122 nucleotides
Theoretical weight: 37.87 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: 3.1Å
Relevant EMDB volumes: EMD-31040
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Structural and functional specificity of H3K36 methylation.
Lam 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)