› 6ugm

Electron Microscopy
3.7Å resolution

Structural basis of COMPASS eCM recognition of an unmodified nucleosome

Released:
DOI: 10.2210/pdb6ugm/pdb
PDB entry 6ugm coloured by chain, front view.
PDB entry 6ugm coloured by chain, side view.
PDB entry 6ugm 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-20765

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-120695 (preferred)
Entry contents:
12 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (14 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
Molecule details ›
Chains: C, G
Length: 107 amino acids
Theoretical weight: 11.69 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6AZJ8 (Residues: 13-119; Coverage: 82%)
Gene names: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L
Sequence domains:
Histone H2B 1.1 Chain: D
Molecule details ›
Chain: D
Length: 125 amino acids
Theoretical weight: 13.85 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 2-126; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H2B 1.1 Chain: H
Molecule details ›
Chain: H
Length: 125 amino acids
Theoretical weight: 13.83 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 2-126; Coverage: 99%)
Sequence domains: Core histone H2A/H2B/H3/H4
Swd3 Chain: K
Molecule details ›
Chain: K
Length: 327 amino acids
Theoretical weight: 36.46 KDa
Source organism: Kluyveromyces lactis NRRL Y-1140
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6CLY5 (Residues: 1-327; Coverage: 100%)
Gene name: KLLA0_E24487g
Sequence domains: WD domain, G-beta repeat
Histone-lysine N-methyltransferase, H3 lysine-4 specific Chain: M
Molecule details ›
Chain: M
Length: 275 amino acids
Theoretical weight: 31.45 KDa
Source organism: Kluyveromyces lactis NRRL Y-1140
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6CIT4 (Residues: 726-1000; Coverage: 28%)
Gene names: KLLA0F24134g, SET1
Sequence domains:
Swd1 Chain: N
Molecule details ›
Chain: N
Length: 439 amino acids
Theoretical weight: 49.89 KDa
Source organism: Kluyveromyces lactis NRRL Y-1140
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6CXF3 (Residues: 1-439; Coverage: 100%)
Gene name: KLLA0_A08800g
Sequence domains: WD domain, G-beta repeat
H3 N-terminus Chain: R
Molecule details ›
Chain: R
Length: 3 amino acids
Theoretical weight: 378 Da
Source organism: Xenopus laevis
Expression system: Escherichia coli
PHD-type domain-containing protein Chain: X
Molecule details ›
Chain: X
Length: 342 amino acids
Theoretical weight: 39.3 KDa
Source organism: Kluyveromyces lactis NRRL Y-1140
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6CRQ4 (Residues: 1-342; Coverage: 100%)
Gene name: KLLA0_D07260g
Sequence domains: PHD-finger
B30.2/SPRY domain-containing protein Chain: L
Molecule details ›
Chain: L
Length: 405 amino acids
Theoretical weight: 47.29 KDa
Source organism: Kluyveromyces lactis NRRL Y-1140
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6CTQ1 (Residues: 1-405; Coverage: 100%)
Gene name: KLLA0_C10945g
Sdc1 Chains: O, P
Molecule details ›
Chains: O, P
Length: 134 amino acids
Theoretical weight: 14.72 KDa
Source organism: Kluyveromyces lactis NRRL Y-1140
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6CPN6 (Residues: 1-134; Coverage: 100%)
Gene name: KLLA0_E03521g
Sequence domains: Dpy-30 motif
DNA (146-MER) Chain: I
Molecule details ›
Chain: I
Length: 147 nucleotides
Theoretical weight: 45.11 KDa
DNA (146-MER) Chain: J
Molecule details ›
Chain: J
Length: 146 nucleotides
Theoretical weight: 45.31 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-20765
Expression systems:
  • Escherichia coli
  • Trichoplusia ni

Quick links

Citations

17 review citations

Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation.
Hughes et al. (2020)
16 more

3 mentions without citation

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