› 5vo0

X-ray diffraction
3.9Å resolution

Structure of a TRAF6-Ubc13~Ub complex

Released:
DOI: 10.2210/pdb5vo0/pdb
PDB entry 5vo0 coloured by chain, front view.
PDB entry 5vo0 coloured by chain, side view.
PDB entry 5vo0 coloured by chain, top view.
Source organisms:
Primary publication:
The activity of TRAF RING homo- and heterodimers is regulated by zinc finger 1.
Middleton AJ, Budhidarmo R, Das A, Zhu J, Foglizzo M, Mace PD, Day CL
Nat Commun 8 1788 (2017)
PMID: 29176576

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
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
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-143301 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
TNF receptor-associated factor 6 Chains: A, D
Molecule details ›
Chains: A, D
Length: 172 amino acids
Theoretical weight: 19.77 KDa
Source organism: Danio rerio
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q6IWL4 (Residues: 50-213; Coverage: 30%)
Gene names: si:dkey-56p7.3, traf6, zgc:63704
Sequence domains:
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Ubiquitin-conjugating enzyme E2 N Chains: B, E
Molecule details ›
Chains: B, E
Length: 157 amino acids
Theoretical weight: 17.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P61088 (Residues: 1-152; Coverage: 100%)
Gene names: BLU, UBE2N
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin Chains: C, F
Molecule details ›
Chains: C, F
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P42212
Unit cell:
a: 181.114Å b: 181.114Å c: 97.414Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.255 0.252 0.299
Expression system: Escherichia coli BL21

Quick links

Citations

5 review citations

TRAF Regulation of IL-17 Cytokine Signaling.
Swaidani et al. (2019)
4 more

4 mentions without citation

Structural Diversity of Ubiquitin E3 Ligase.
Toma-Fukai et al. (2021)
3 more