› 1r4n

X-ray diffraction
3.6Å resolution

APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP

Released:
DOI: 10.2210/pdb1r4n/pdb
PDB entry 1r4n coloured by chain, front view.
PDB entry 1r4n coloured by chain, side view.
PDB entry 1r4n coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1.
Walden H, Podgorski MS, Huang DT, Miller DW, Howard RJ, Minor DL, Holton JM, Schulman BA
Mol Cell 12 1427-37 (2003)
PMID: 14690597

Function and Biology Details

Reaction catalysed: 
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine = AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171762 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
NEDD8-activating enzyme E1 regulatory subunit Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 529 amino acids
Theoretical weight: 59.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13564 (Residues: 1-534; Coverage: 99%)
Gene names: APPBP1, HPP1, NAE1
Sequence domains: ThiF family
Structure domains: NAD(P)-binding Rossmann-like Domain
NEDD8-activating enzyme E1 catalytic subunit Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 431 amino acids
Theoretical weight: 48.39 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 Chains: I, J, K, L
Molecule details ›
Chains: I, J, K, L
Length: 76 amino acids
Theoretical weight: 8.57 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

2 bound ligands:
Ligand ATP 4 x ATP
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 135Å b: 197.9Å c: 211Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.285 0.251 0.29
Expression system: Escherichia coli

Quick links

Citations

48 review citations

Ubiquitin: structures, functions, mechanisms.
Pickart et al. (2004)
47 more

15 mentions without citation

Taking it step by step: mechanistic insights from structural studies of ubiquitin/ubiquitin-like protein modification pathways.
Capili et al. (2007)
14 more