› 4lcd

X-ray diffraction
3.1Å resolution

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

Released:
DOI: 10.2210/pdb4lcd/pdb
PDB entry 4lcd coloured by chain, front view.
PDB entry 4lcd coloured by chain, side view.
PDB entry 4lcd coloured by chain, top view.
Source organisms:
Primary publication:
Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3.
Kamadurai HB, Qiu Y, Deng A, Harrison JS, Macdonald C, Actis M, Rodrigues P, Miller DJ, Souphron J, Lewis SM, Kurinov I, Fujii N, Hammel M, Piper R, Kuhlman B, Schulman BA
Elife 2 e00828 (2013)
PMID: 23936628

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)
PDBe Complex ID:
PDB-CPX-143338 (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

Quick links

Citations

26 review citations

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

13 mentions without citation

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