› 6cct

X-ray diffraction
2.4Å resolution

Fragment of GID4 in complex with a short peptide

Released:
DOI: 10.2210/pdb6cct/pdb
PDB entry 6cct coloured by chain, front view.
PDB entry 6cct coloured by chain, side view.
PDB entry 6cct coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis of GID4-mediated recognition of degrons for the Pro/N-end rule pathway.
Dong C, Zhang H, Li L, Tempel W, Loppnau P, Min J
Nat Chem Biol 14 466-473 (2018)
PMID: 29632410

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166511 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Glucose-induced degradation protein 4 homolog Chain: A
Molecule details ›
Chain: A
Length: 167 amino acids
Theoretical weight: 19.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IVV7 (Residues: 124-289; Coverage: 55%)
Gene names: C17orf39, GID4, VID24
Sequence domains: Vacuolar import and degradation protein
Tetrapeptide Chain: B
Molecule details ›
Chain: B
Length: 4 amino acids
Theoretical weight: 429 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P41212
Unit cell:
a: 40.14Å b: 40.14Å c: 203.343Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.218 0.26
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

N-degron and C-degron pathways of protein degradation.
Varshavsky A. (2019)
8 more

1 mention without citation

Cryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation.
Qiao et al. (2022)