PDBe 3dbh

X-ray diffraction
2.85Å resolution

Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Ala-NEDD8Ala72Arg)

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
NEDD8 Chains: I, J, K, L
Molecule details ›
Chains: I, J, K, L
Length: 88 amino acids
Theoretical weight: 9.72 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
NEDD8-activating enzyme E1 catalytic subunit Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 434 amino acids
Theoretical weight: 48.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TBC4 (Residues: 33-463; Coverage: 93%)
Gene names: UBA3, UBE1C
Sequence domains:
Structure domains:
NEDD8-activating enzyme E1 regulatory subunit Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 531 amino acids
Theoretical weight: 59.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13564 (Residues: 1-534; Coverage: 99%)
Gene names: APPBP1, HPP1, NAE1
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 135.647Å b: 198.1Å c: 210.961Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.224 0.274
Expression system: Escherichia coli