7mex

Electron Microscopy
3.35Å resolution

Structure of yeast Ubr1 in complex with Ubc2 and N-degron

Released:
Related structures: EMD-23806

Function and Biology Details

Reactions catalysed:
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-138870 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ubiquitin Chain: C
Molecule details ›
Chain: C
Length: 76 amino acids
Theoretical weight: 8.62 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Ubiquitin-conjugating enzyme E2 2 Chain: B
Molecule details ›
Chain: B
Length: 150 amino acids
Theoretical weight: 17.2 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P06104 (Residues: 3-152; Coverage: 87%)
Gene names: RAD6, UBC2, YGL058W
Sequence domains: Ubiquitin-conjugating enzyme
N-degron Chain: D
Molecule details ›
Chain: D
Length: 43 amino acids
Theoretical weight: 4.57 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided
E3 ubiquitin-protein ligase UBR1 Chain: A
Molecule details ›
Chain: A
Length: 1950 amino acids
Theoretical weight: 225.1 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P19812 (Residues: 1-1950; Coverage: 100%)
Gene names: G7168, PTR1, UBR1, YGR184C
Sequence domains:

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.35Å
Relevant EMDB volumes: EMD-23806
Expression systems:
  • Not provided
  • Saccharomyces cerevisiae S288C