› 4be8

X-ray diffraction
3Å resolution

NEDD4 HECT A889F structure

Released:
DOI: 10.2210/pdb4be8/pdb
PDB entry 4be8 coloured by chain, front view.
PDB entry 4be8 coloured by chain, side view.
PDB entry 4be8 coloured by chain, top view.
Source organism: Homo sapiens
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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155546 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase NEDD4 Chain: A
Molecule details ›
Chain: A
Length: 385 amino acids
Theoretical weight: 45.71 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:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P3121
Unit cell:
a: 100.545Å b: 100.545Å c: 96.45Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.248 0.246 0.295
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

32 review citations

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

3 mentions without citation

An approach to creating a more realistic working model from a protein data bank entry.
Brandon et al. (2015)
2 more