› 5ifr

X-ray diffraction
2.2Å resolution

Structure of the stable UBE2D3-UbDha conjugate

Released:
DOI: 10.2210/pdb5ifr/pdb
PDB entry 5ifr coloured by chain, front view.
PDB entry 5ifr coloured by chain, side view.
PDB entry 5ifr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A cascading activity-based probe sequentially targets E1-E2-E3 ubiquitin enzymes.
Mulder MP, Witting K, Berlin I, Pruneda JN, Wu KP, Chang JG, Merkx R, Bialas J, Groettrup M, Vertegaal AC, Schulman BA, Komander D, Neefjes J, El Oualid F, Ovaa H
Nat Chem Biol 12 523-30 (2016)
PMID: 27182664

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143253 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-conjugating enzyme E2 D3 Chain: A
Molecule details ›
Chain: A
Length: 151 amino acids
Theoretical weight: 16.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61077 (Residues: 2-147; Coverage: 99%)
Gene names: UBC5C, UBCH5C, UBE2D3
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21
Unit cell:
a: 42.125Å b: 52.271Å c: 53.624Å
α: 90° β: 100.78° γ: 90°
R-values:
R R work R free
0.194 0.191 0.244
Expression system: Escherichia coli

Quick links

Citations

28 review citations

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

3 mentions without citation

Proteolysis-Targeting Chimeras as Therapeutics and Tools for Biological Discovery.
Burslem et al. (2020)
2 more