› 6ven

Electron Microscopy
3.37Å resolution

Yeast COMPASS in complex with a ubiquitinated nucleosome

Released:
DOI: 10.2210/pdb6ven/pdb
PDB entry 6ven coloured by chain, front view.
PDB entry 6ven coloured by chain, side view.
PDB entry 6ven coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for COMPASS recognition of an H2B-ubiquitinated nucleosome.
Worden EJ, Zhang X, Wolberger C
Elife 9 (2020)
PMID: 31922488
Related structures: EMD-21157

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-120755 (preferred)
Entry contents:
11 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (13 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
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
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 BL21(DE3)
UniProt:
  • Canonical: P62799 (Residues: 2-103; Coverage: 99%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
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:
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 BL21(DE3)
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
Ubiquitin Chain: K
Molecule details ›
Chain: K
Length: 80 amino acids
Theoretical weight: 9.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
COMPASS component SWD3 Chain: L
Molecule details ›
Chain: L
Length: 315 amino acids
Theoretical weight: 34.79 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P38123 (Residues: 1-315; Coverage: 100%)
Gene names: CPS30, SAF35, SWD3, YBR1237, YBR175W
Sequence domains: WD domain, G-beta repeat
COMPASS component SWD1 Chain: M
Molecule details ›
Chain: M
Length: 426 amino acids
Theoretical weight: 48.7 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P39706 (Residues: 1-426; Coverage: 100%)
Gene names: CPS50, FUN16, SAF49, SWD1, YAR003W
Sequence domains: WD domain, G-beta repeat
Histone-lysine N-methyltransferase, H3 lysine-4 specific Chain: N
Molecule details ›
Chain: N
Length: 358 amino acids
Theoretical weight: 41.51 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P38827 (Residues: 762-1080; Coverage: 30%)
Gene names: KMT2, SET1, YHR119W, YTX1
Sequence domains:
COMPASS component BRE2 Chain: O
Molecule details ›
Chain: O
Length: 505 amino acids
Theoretical weight: 58.43 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P43132 (Residues: 1-505; Coverage: 100%)
Gene names: BRE2, CPS60, YLR015W
COMPASS component SDC1 Chains: P, Q
Molecule details ›
Chains: P, Q
Length: 175 amino acids
Theoretical weight: 19.47 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q03323 (Residues: 1-175; Coverage: 100%)
Gene names: CPS25, SAF19, SDC1, YDR469W
Sequence domains: Dpy-30 motif
COMPASS component SPP1 Chain: R
Molecule details ›
Chain: R
Length: 391 amino acids
Theoretical weight: 45.49 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q03012 (Residues: 2-353; Coverage: 100%)
Gene names: CPS40, SAF41, SPP1, YPL138C
Sequence domains: PHD-finger
601 DNA (146-MER) Chain: I
Molecule details ›
Chain: I
Length: 146 nucleotides
Theoretical weight: 44.83 KDa
601 DNA (146-MER) Chain: J
Molecule details ›
Chain: J
Length: 146 nucleotides
Theoretical weight: 45.31 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand SAM 1 x SAM
1 modified residue:
Ligand NLE 6 x NLE

Experiments and Validation Details

Entry percentile scores
Resolution: 3.37Å
Relevant EMDB volumes: EMD-21157
Expression systems:
  • Escherichia coli
  • Escherichia coli BL21(DE3)
  • Trichoplusia ni

Quick links

Citations

16 review citations

Histone Monoubiquitination in Chromatin Remodelling: Focus on the Histone H2B Interactome and Cancer.
Marsh et al. (2020)
15 more

7 mentions without citation

Principles of nucleosome recognition by chromatin factors and enzymes.
McGinty et al. (2021)
6 more