› 6t9l

Electron Microscopy
3.6Å resolution

SAGA DUB module bound to a ubiqitinated nucleosome

Released:
DOI: 10.2210/pdb6t9l/pdb
PDB entry 6t9l coloured by chain, front view.
PDB entry 6t9l coloured by chain, side view.
PDB entry 6t9l coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the transcription coactivator SAGA.
Wang H, Dienemann C, Stützer A, Urlaub H, Cheung ACM, Cramer P
Nature 577 717-720 (2020)
PMID: 31969703
Related structures: EMD-10415

Function and Biology Details

Reaction catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
PDBe Complex ID:
PDB-CPX-120641 (preferred)
Entry contents:
10 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (12 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
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 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 Chain: D
Molecule details ›
Chain: D
Length: 122 amino acids
Theoretical weight: 13.52 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
Histone H2B 1.1 Chain: H
Molecule details ›
Chain: H
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
Ubiquitin carboxyl-terminal hydrolase 8 Chain: K
Molecule details ›
Chain: K
Length: 471 amino acids
Theoretical weight: 53.69 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P50102 (Residues: 1-471; Coverage: 100%)
Gene names: UBP8, YM9959.05, YMR223W
Sequence domains:
Transcription and mRNA export factor SUS1 Chain: L
Molecule details ›
Chain: L
Length: 96 amino acids
Theoretical weight: 11.09 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q6WNK7 (Residues: 1-96; Coverage: 100%)
Gene names: SUS1, YBR111W-A
Sequence domains: Transcription factor e(y)2
SAGA-associated factor 11 Chain: M
Molecule details ›
Chain: M
Length: 99 amino acids
Theoretical weight: 11.3 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q03067 (Residues: 1-99; Coverage: 100%)
Gene names: SGF11, YPL047W
Sequence domains:
SAGA-associated factor 73 Chain: N
Molecule details ›
Chain: N
Length: 657 amino acids
Theoretical weight: 72.98 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53165 (Residues: 1-657; Coverage: 100%)
Gene names: SGF73, YGL066W
Sequence domains:
Ubiquitin Chain: O
Molecule details ›
Chain: O
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Widom601 DNA (145-MER) Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.52 KDa
Widom601 DNA (145-MER) Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.99 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-10415
Expression systems:
  • Escherichia coli
  • Saccharomyces cerevisiae S288C

Quick links

Citations

13 review citations

Structure and mechanism of the RNA polymerase II transcription machinery.
Schier et al. (2020)
12 more

3 mentions without citation

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