6j99

Electron Microscopy
4.1Å resolution

Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome

Released:

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)
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-104611 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
Histone H3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A310TTQ1 (Residues: 1-136; Coverage: 100%)
Gene names: LOC108703785, LOC121398065, LOC121398067
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A Chains: C, G
Molecule details ›
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6AZJ8 (Residues: 1-130; Coverage: 100%)
Gene names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
Sequence domains:
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 123 amino acids
Theoretical weight: 13.63 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
Ubiquitin Chain: L
Molecule details ›
Chain: L
Length: 76 amino acids
Theoretical weight: 8.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62979 (Residues: 1-76; Coverage: 49%)
Gene names: RPS27A, UBA80, UBCEP1
Sequence domains: Ubiquitin family
Histone-lysine N-methyltransferase, H3 lysine-79 specific Chain: K
Molecule details ›
Chain: K
Length: 416 amino acids
Theoretical weight: 47.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TEK3 (Residues: 1-416; Coverage: 27%)
Gene names: DOT1L, KIAA1814, KMT4
Sequence domains: Histone methylation protein DOT1
DNA (144-MER) Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.14 KDa
DNA (145-MER) Chain: J
Molecule details ›
Chain: J
Length: 147 nucleotides
Theoretical weight: 45.61 KDa

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-9783
Expression system: Escherichia coli