PDBe 3jvz

X-ray diffraction
3.3Å resolution

Function and Biology Details

Reactions catalysed:
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
(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
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 146 amino acids
Theoretical weight: 16.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 2-147; Coverage: 99%)
  • Best match: P62837-2 (Residues: 1-118)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
E3 ubiquitin-protein ligase NEDD4-like Chains: C, D
Molecule details ›
Chains: C, D
Length: 385 amino acids
Theoretical weight: 45.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96PU5 (Residues: 596-975; Coverage: 39%)
Gene names: KIAA0439, NEDD4L, NEDL3
Sequence domains: HECT-domain (ubiquitin-transferase)
Structure domains:
Ubiquitin Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 81 amino acids
Theoretical weight: 8.92 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
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: APS BEAMLINE 24-ID-C
Spacegroup: C2221
Unit cell:
a: 173.98Å b: 199.888Å c: 109.707Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.217 0.267
Expression system: Escherichia coli