› 6cd8

X-ray diffraction
1.6Å resolution

Complex of GID4 fragment with short peptide

Released:
DOI: 10.2210/pdb6cd8/pdb
PDB entry 6cd8 coloured by chain, front view.
PDB entry 6cd8 coloured by chain, side view.
PDB entry 6cd8 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-166513 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Glucose-induced degradation protein 4 homolog Chains: A, B
Molecule details ›
Chains: A, B
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 PSRV Chains: C, D
Molecule details ›
Chains: C, D
Length: 4 amino acids
Theoretical weight: 459 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand UNX 19 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P6522
Unit cell:
a: 63.941Å b: 63.941Å c: 289.593Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.198 0.197 0.224
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)