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› 6uh5

Electron Microscopy
3.5Å resolution

Structural basis of COMPASS eCM recognition of the H2Bub nucleosome

Released:
DOI: 10.2210/pdb6uh5/pdb
PDB entry 6uh5 coloured by chain, front view.
PDB entry 6uh5 coloured by chain, side view.
PDB entry 6uh5 coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS.
Hsu PL, Shi H, Leonen C, Kang J, Chatterjee C, Zheng N
Mol Cell 76 712-723.e4 (2019)
PMID: 31733991
Related structures: EMD-20767

Function and Biology Details

Reaction catalysed: 
L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-methionine = N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-homocysteine + 3 H(+).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonadecamer (preferred)
PDBe Complex ID:
PDB-CPX-120696 (preferred)
Entry contents:
13 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (15 distinct):
Histone H3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.28 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q92133 (Residues: 2-136; Coverage: 99%)
Gene names: H3l, Hist1h3f, h3, h3.2a, h3c8, h3c8.S, h3r, hist1h3g, hist1h3g.L, hist2h3, hist2h3c
Sequence domains: Core histone H2A/H2B/H3/H4
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
Histone H2A Chains: C, G
Histone H2B 1.1 Chain: D
Histone H2B 1.1 Chain: H
Swd3 Chain: K
Histone-lysine N-methyltransferase, H3 lysine-4 specific Chain: M
Swd1 Chain: N
Ubiquitin Chain: Q
Histone H3.2 Chain: R
PHD-type domain-containing protein Chain: X
B30.2/SPRY domain-containing protein Chain: L
Sdc1 Chains: O, P
DNA (146-MER) Chain: I
DNA (146-MER) Chain: J

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand SAM 1 x SAM
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.5Å
Relevant EMDB volumes: EMD-20767
Expression systems:
  • Escherichia coli
  • Trichoplusia ni

Quick links

Citations

20 review citations

An expanded lexicon for the ubiquitin code.
Dikic et al. (2023)
19 more

4 mentions without citation

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