› 4bbn

X-ray diffraction
2.51Å resolution

NEDD4 HECT-Ub:Ub complex

Released:
DOI: 10.2210/pdb4bbn/pdb
PDB entry 4bbn coloured by chain, front view.
PDB entry 4bbn coloured by chain, side view.
PDB entry 4bbn coloured by chain, top view.
Source organisms:
Primary publication:
Structure of a ubiquitin-loaded HECT ligase reveals the molecular basis for catalytic priming.
Maspero E, Valentini E, Mari S, Cecatiello V, Soffientini P, Pasqualato S, Polo S
Nat Struct Mol Biol 20 696-701 (2013)
PMID: 23644597

Function and Biology Details

Reaction catalysed: 
(1a) S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + S-ubiquitinyl-[HECT-type E3 ubiquitin transferase]-L-cysteine
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143460 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase NEDD4 Chain: A
Molecule details ›
Chain: A
Length: 385 amino acids
Theoretical weight: 45.63 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P46934 (Residues: 938-1319; Coverage: 29%)
Gene names: KIAA0093, NEDD4, NEDD4-1, PIG53, RPF1
Sequence domains: HECT-domain (ubiquitin-transferase)
Structure domains:
Ubiquitin Chain: C
Molecule details ›
Chain: C
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Bos taurus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG53 (Residues: 229-304; Coverage: 25%)
Gene name: UBB
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Ubiquitin Chain: F
Molecule details ›
Chain: F
Length: 76 amino acids
Theoretical weight: 8.62 KDa
Source organism: Bos taurus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CG53 (Residues: 229-304; Coverage: 25%)
Gene name: UBB
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: R32
Unit cell:
a: 196.54Å b: 196.54Å c: 98.77Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.179 0.176 0.224
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

26 review citations

Ubiquitin Ligases: Structure, Function, and Regulation.
Zheng et al. (2017)
25 more

20 mentions without citation

Structural insights into the catalysis and regulation of E3 ubiquitin ligases.
Buetow et al. (2016)
19 more