PDBe 2nvu

X-ray diffraction
2.8Å resolution

Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
NEDD8-activating enzyme E1 regulatory subunit Chain: A
Molecule details ›
Chain: A
Length: 536 amino acids
Theoretical weight: 60.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13564 (Residues: 1-534; Coverage: 100%)
Gene names: APPBP1, HPP1, NAE1
Sequence domains: ThiF family
Structure domains: NAD(P)-binding Rossmann-like Domain
NEDD8-activating enzyme E1 catalytic subunit Chain: B
Molecule details ›
Chain: B
Length: 805 amino acids
Theoretical weight: 89.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TBC4 (Residues: 31-463; Coverage: 94%)
Gene names: UBA3, UBE1C
Sequence domains:
Structure domains:
NEDD8-conjugating enzyme Ubc12 Chain: C
Molecule details ›
Chain: C
Length: 180 amino acids
Theoretical weight: 20.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61081 (Residues: 1-183; Coverage: 97%)
Gene names: UBC12, UBE2M
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
NEDD8 Chains: I, J
Molecule details ›
Chains: I, J
Length: 81 amino acids
Theoretical weight: 8.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15843 (Residues: 1-76; Coverage: 94%)
Gene name: NEDD8
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P3221
Unit cell:
a: 156.494Å b: 156.494Å c: 190.485Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.241 0.241 0.274
Expression system: Escherichia coli