8pmq

Electron Microscopy
3.53Å resolution

Catalytic module of yeast GID E3 ligase bound to multiphosphorylated Ubc8~ubiquitin

Released:

Function and Biology Details

Reactions catalysed:
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
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
Biochemical function:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-279607 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
E3 ubiquitin-protein ligase RMD5 Chain: 2
Molecule details ›
Chain: 2
Length: 421 amino acids
Theoretical weight: 49.24 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q12508 (Residues: 1-421; Coverage: 100%)
Gene names: GID2, RMD5, YD9320A.05c, YDR255C
Sequence domains: CTLH/CRA C-terminal to LisH motif domain
Protein FYV10 Chain: 9
Molecule details ›
Chain: 9
Length: 516 amino acids
Theoretical weight: 59.98 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P40492 (Residues: 1-516; Coverage: 100%)
Gene names: FYV10, GID9, YIL097W
Sequence domains: CTLH/CRA C-terminal to LisH motif domain
Ubiquitin-conjugating enzyme E2-24 kDa Chain: E
Ubiquitin Chain: U

Ligands and Environments

1 bound ligand:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
Resolution: 3.53Å
Relevant EMDB volumes: EMD-17764
Expression systems:
  • Trichoplusia ni
  • Escherichia coli