› 3oj4

X-ray diffraction
3.4Å resolution

Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex

Released:
DOI: 10.2210/pdb3oj4/pdb
PDB entry 3oj4 coloured by chain, front view.
PDB entry 3oj4 coloured by chain, side view.
PDB entry 3oj4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling.
Bosanac I, Wertz IE, Pan B, Yu C, Kusam S, Lam C, Phu L, Phung Q, Maurer B, Arnott D, Kirkpatrick DS, Dixit VM, Hymowitz SG
Mol Cell 40 548-57 (2010)
PMID: 21095585

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
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-143344 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 D1 Chains: A, D
Molecule details ›
Chains: A, D
Length: 153 amino acids
Theoretical weight: 17.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P51668 (Residues: 1-147; Coverage: 100%)
Gene names: SFT, UBC5A, UBCH5, UBCH5A, UBE2D1
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin Chains: B, E
Molecule details ›
Chains: B, E
Length: 79 amino acids
Theoretical weight: 8.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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
A20p37 Chains: C, F
Molecule details ›
Chains: C, F
Length: 49 amino acids
Theoretical weight: 5.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P21580 (Residues: 592-635; Coverage: 6%)
Gene names: OTUD7C, TNFAIP3

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P321
Unit cell:
a: 102.646Å b: 102.646Å c: 112.686Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.284 0.28 0.319
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

42 review citations

The ubiquitin code.
Komander et al. (2012)
41 more

3 mentions without citation

Regulation of proteolysis by human deubiquitinating enzymes.
Eletr et al. (2014)
2 more