› 6jm9

Electron Microscopy
7.3Å resolution

cryo-EM structure of DOT1L bound to unmodified nucleosome

Released:
DOI: 10.2210/pdb6jm9/pdb
PDB entry 6jm9 coloured by chain, front view.
PDB entry 6jm9 coloured by chain, side view.
PDB entry 6jm9 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase.
Jang S, Kang C, Yang HS, Jung T, Hebert H, Chung KY, Kim SJ, Hohng S, Song JJ
Genes Dev 33 620-625 (2019)
PMID: 30923167
Related structures: EMD-9843

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 undecamer (preferred)
PDBe Complex ID:
PDB-CPX-120081 (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: 98 amino acids
Theoretical weight: 11.49 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P84233 (Residues: 39-136; Coverage: 72%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 87 amino acids
Theoretical weight: 9.99 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P62799 (Residues: 17-103; Coverage: 85%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A Chains: C, G
Molecule details ›
Chains: C, G
Length: 107 amino acids
Theoretical weight: 11.72 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q6AZJ8 (Residues: 15-121; Coverage: 82%)
Gene names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
Sequence domains:
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 94 amino acids
Theoretical weight: 10.48 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P02281 (Residues: 34-126; Coverage: 74%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone-lysine N-methyltransferase, H3 lysine-79 specific Chain: X
Molecule details ›
Chain: X
Length: 328 amino acids
Theoretical weight: 37.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q8TEK3 (Residues: 5-332; Coverage: 21%)
Gene names: DOT1L, KIAA1814, KMT4
Sequence domains: Histone methylation protein DOT1
DNA strand I Chain: I
Molecule details ›
Chain: I
Length: 123 nucleotides
Theoretical weight: 37.89 KDa
DNA strand J Chain: J
Molecule details ›
Chain: J
Length: 123 nucleotides
Theoretical weight: 38.01 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 7.3Å
Relevant EMDB volumes: EMD-9843
Expression system: Escherichia coli BL21

Quick links

Citations

13 review citations

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

1 mention without citation

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