› 7k6p

Electron Microscopy
3.2Å resolution

Active state Dot1 bound to the unacetylated H4 nucleosome

Released:
DOI: 10.2210/pdb7k6p/pdb
PDB entry 7k6p coloured by chain, front view.
PDB entry 7k6p coloured by chain, side view.
PDB entry 7k6p coloured by chain, top view.
Source organisms:
Primary publication:
Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation.
Valencia-Sánchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ
Science 371 (2021)
PMID: 33479126
Related structures: EMD-22691

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(79) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(79)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-121440 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 98 amino acids
Theoretical weight: 11.56 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 38-135; Coverage: 72%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 90 amino acids
Theoretical weight: 10.18 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 14-103; Coverage: 87%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: C, G
Histone H2B 1.1 Chains: D, H
Histone-lysine N-methyltransferase, H3 lysine-79 specific Chain: K
Ubiquitin Chain: L
DNA (146-MER) Chain: I
DNA (146-MER) Chain: J

Ligands and Environments

1 bound ligand:
Ligand SAM 1 x SAM
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.2Å
Relevant EMDB volumes: EMD-22691
Expression system: Escherichia coli

Quick links

Citations

17 review citations

The language of chromatin modification in human cancers.
Zhao et al. (2021)
16 more

2 mentions without citation

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