PDBe 4lcd

X-ray diffraction
3.1Å resolution

Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3

Released:

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
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase RSP5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 432 amino acids
Theoretical weight: 50.47 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P39940 (Residues: 383-809; Coverage: 53%)
Gene names: MDP1, NPI1, RSP5, SYGP-ORF41, YER125W
Sequence domains:
Protein SNA3 Chains: C, D
Molecule details ›
Chains: C, D
Length: 24 amino acids
Theoretical weight: 2.56 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided
UniProt:
  • Canonical: P14359 (Residues: 104-127; Coverage: 18%)
Gene names: J0630, SNA3, YJL151C
Ubiquitin Chains: E, F
Molecule details ›
Chains: E, F
Length: 83 amino acids
Theoretical weight: 9.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-683; 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: P21
Unit cell:
a: 83.046Å b: 78.923Å c: 96.722Å
α: 90° β: 101.67° γ: 90°
R-values:
R R work R free
0.253 0.251 0.299
Expression systems:
  • Escherichia coli
  • Not provided