› 6jwi

X-ray diffraction
2.55Å resolution

Yeast Npl4 in complex with Lys48-linked diubiquitin

Released:
DOI: 10.2210/pdb6jwi/pdb
PDB entry 6jwi coloured by chain, front view.
PDB entry 6jwi coloured by chain, side view.
PDB entry 6jwi coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4.
Sato Y, Tsuchiya H, Yamagata A, Okatsu K, Tanaka K, Saeki Y, Fukai S
OpenAccess logo Nat Commun 10 5708 (2019)
PMID: 31836717

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-152643 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin Chains: G, I
Molecule details ›
Chains: G, I
Length: 76 amino acids
Theoretical weight: 8.62 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P62984 (Residues: 1-76; Coverage: 59%)
Gene names: Uba52, Ubcep2
Sequence domains: Ubiquitin family
Nuclear protein localization protein 4 Chains: A, E
Molecule details ›
Chains: A, E
Length: 473 amino acids
Theoretical weight: 53.94 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P33755 (Residues: 113-580; Coverage: 81%)
Gene names: HRD4, NPL4, YBR1231, YBR170C
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC
Carbohydrate polymer
2 bound ligands:
Ligand ZN 4 x ZN
Ligand BCN 9 x BCN
1 modified residue:
Ligand MSE 2 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 86.351Å b: 103.103Å c: 99.62Å
α: 90° β: 100.401° γ: 90°
R-values:
R R work R free
0.192 0.19 0.226
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Order through destruction: how ER-associated protein degradation contributes to organelle homeostasis.
Christianson et al. (2022)
8 more