› 7k5j

X-ray diffraction
3.42Å resolution

Structure of an E1-E2-ubiquitin thioester mimetic

Released:
DOI: 10.2210/pdb7k5j/pdb
PDB entry 7k5j coloured by chain, front view.
PDB entry 7k5j coloured by chain, side view.
PDB entry 7k5j coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of an E1-E2-ubiquitin thioester mimetic reveal molecular mechanisms of transthioesterification.
Yuan L, Lv Z, Adams MJ, Olsen SK
Nat Commun 12 2370 (2021)
PMID: 33888705

Function and Biology Details

Reactions catalysed: 
ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine = AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine
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 trimer (preferred)
PDBe Complex ID:
PDB-CPX-147028 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin Chains: M, N, O, P, Q, R, W, X
Molecule details ›
Chains: M, N, O, P, Q, R, W, X
Length: 83 amino acids
Theoretical weight: 9.69 KDa
Source organism: Triticum aestivum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P69326 (Residues: 1-76; Coverage: 99%)
Sequence domains: Ubiquitin family
Ubiquitin-activating enzyme E1 1 Chains: A, C, D, G, I, K, S, U
Molecule details ›
Chains: A, C, D, G, I, K, S, U
Length: 1017 amino acids
Theoretical weight: 113.7 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P22515 (Residues: 11-1024; Coverage: 99%)
Gene names: UBA1, YKL210W
Sequence domains:
Ubiquitin-conjugating enzyme E2-34 kDa Chains: B, E, F, H, J, L, T, V
Molecule details ›
Chains: B, E, F, H, J, L, T, V
Length: 197 amino acids
Theoretical weight: 22.49 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P14682 (Residues: 3-195; Coverage: 65%)
Gene names: CDC34, D4211, DNA6, UBC3, YD9609.08C, YDR054C
Sequence domains: Ubiquitin-conjugating enzyme

Ligands and Environments

1 bound ligand:
Ligand AMP 7 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 95.181Å b: 272.917Å c: 258.342Å
α: 90° β: 94.59° γ: 90°
R-values:
R R work R free
0.203 0.203 0.246
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 citation in other articles

Structure of UBE2K-Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension.
Nakasone et al. (2022)
3 more

1 mention without citation

Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer.
Afsar et al. (2023)