› 6nj9

Electron Microscopy
2.96Å resolution

Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex

Released:
DOI: 10.2210/pdb6nj9/pdb
PDB 6nj9 coloured by chain and viewed from the front.
PDB 6nj9 coloured by chain and viewed from the side.
PDB 6nj9 coloured by chain and viewed from the top.
Source organisms:
Primary publication:
Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L.
Worden EJ, Hoffmann NA, Hicks CW, Wolberger C
Cell (2019)
PMID: 30765112
Related structures: EMD-9384

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:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetradecamer (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: 135 amino acids
Theoretical weight: 15.25 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 102 amino acids
Theoretical weight: 11.26 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 122 amino acids
Theoretical weight: 13.5 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone-lysine N-methyltransferase, H3 lysine-79 specific Chains: K, M
Molecule details ›
Chains: K, M
Length: 416 amino acids
Theoretical weight: 47.43 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TEK3 (Residues: 2-416; Coverage: 27%)
Gene names: DOT1L, KIAA1814, KMT4
Sequence domains: Histone methylation protein DOT1
Structure domains:
Ubiquitin Chains: L, N
Molecule details ›
Chains: L, N
Length: 80 amino acids
Theoretical weight: 9.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family
601 DNA Strand 1 Chain: I
Molecule details ›
Chain: I
Length: 146 nucleotides
Theoretical weight: 44.83 KDa
601 DNA Strand 2 Chain: J
Molecule details ›
Chain: J
Length: 146 nucleotides
Theoretical weight: 45.31 KDa

Ligands and Environments

1 bound ligand:
Ligand SAM 2 x SAM
1 modified residue:
Ligand NLE 6 x NLE

Experiments and Validation Details

Entry percentile scores
Resolution: 2.96Å
Relevant EMDB volumes: EMD-9384
Expression systems:
  • Escherichia coli BL21
  • Escherichia coli

Quick links

Citations

24 review citations

BRCA1/BARD1 is a nucleosome reader and writer.
Witus et al. (2022)
23 more

10 mentions without citation

Chromatin Regulation through Ubiquitin and Ubiquitin-like Histone Modifications.
Vaughan et al. (2021)
9 more