› 5jne

X-ray diffraction
2.85Å resolution

E2-SUMO-Siz1 E3-SUMO-PCNA complex

Released:
DOI: 10.2210/pdb5jne/pdb
PDB entry 5jne coloured by chain, front view.
PDB entry 5jne coloured by chain, side view.
PDB entry 5jne coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Capturing a substrate in an activated RING E3/E2-SUMO complex.
Streich FC, Lima CD
Nature 536 304-8 (2016)
PMID: 27509863

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-147507 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
E3 SUMO-protein ligase SIZ1; Ubiquitin-like protein SMT3 Chains: A, E
Molecule details ›
Chains: A, E
Length: 367 amino acids
Theoretical weight: 42.2 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q04195 (Residues: 167-445; Coverage: 31%)
  • Canonical: Q12306 (Residues: 20-98; Coverage: 78%)
Gene names: D9719.15, SIZ1, SMT3, ULL1, YDR409W, YDR510W
Sequence domains:
SUMO-conjugating enzyme UBC9 Chains: B, F
Molecule details ›
Chains: B, F
Length: 160 amino acids
Theoretical weight: 18.29 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P50623 (Residues: 1-157; Coverage: 100%)
Gene names: UBC9, YDL064W
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin-like protein SMT3 Chains: C, G
Molecule details ›
Chains: C, G
Length: 84 amino acids
Theoretical weight: 9.72 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12306 (Residues: 19-98; Coverage: 79%)
Gene names: D9719.15, SMT3, YDR510W
Sequence domains: Ubiquitin family
Proliferating cell nuclear antigen Chains: D, H
Molecule details ›
Chains: D, H
Length: 258 amino acids
Theoretical weight: 28.82 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P15873 (Residues: 1-258; Coverage: 100%)
Gene names: POL30, YBR0811, YBR088C
Sequence domains:
Structure domains: Proliferating Cell Nuclear Antigen

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand GOL 10 x GOL
Ligand 6LN 2 x 6LN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: C2
Unit cell:
a: 93.421Å b: 205.882Å c: 142.501Å
α: 90° β: 95.3° γ: 90°
R-values:
R R work R free
0.214 0.212 0.25
Expression system: Escherichia coli

Quick links

Citations

12 review citations

SUMO-Mediated Regulation of Nuclear Functions and Signaling Processes.
Zhao X. (2018)
11 more

10 mentions without citation

Ubiquitin-like Protein Conjugation: Structures, Chemistry, and Mechanism.
Cappadocia et al. (2018)
9 more