› 6nog

Electron Microscopy
3.9Å resolution

Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome

Released:
DOI: 10.2210/pdb6nog/pdb
PDB entry 6nog coloured by chain, front view.
PDB entry 6nog coloured by chain, side view.
PDB entry 6nog coloured by chain, top view.
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 176 1490-1501.e12 (2019)
PMID: 30765112
Related structures: EMD-0468

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-120350 (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: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
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
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
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
Ubiquitin-like domain-containing protein Chain: L
Molecule details ›
Chain: L
Length: 80 amino acids
Theoretical weight: 9.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: J3QS39 (Residues: 1-76; Coverage: 82%)
Gene name: UBB
Sequence domains: Ubiquitin family
Histone-lysine N-methyltransferase, H3 lysine-79 specific Chain: K
Molecule details ›
Chain: K
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:
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

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-0468
Expression system: Escherichia coli

Quick links

Citations

39 review citations

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

8 mentions without citation

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