› 9b59

Electron Microscopy
3.49Å resolution

Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 5

Released:
DOI: 10.2210/pdb9b59/pdb
PDB entry 9b59 coloured by chain, front view.
PDB entry 9b59 coloured by chain, side view.
PDB entry 9b59 coloured by chain, top view.
Source organism: Schizosaccharomyces pombe 972h-
Primary publication:
Structural basis for transthiolation intermediates in the ubiquitin pathway.
Kochańczyk T, Hann ZS, Lux MC, Delos Reyes AMV, Ji C, Tan DS, Lima CD
Nature (2024)
PMID: 39143218
Related structures: EMD-44204

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-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [HECT-type E3 ubiquitin transferase]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + S-ubiquitinyl-[HECT-type E3 ubiquitin transferase]-L-cysteine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-245061 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 4 Chain: A
Molecule details ›
Chain: A
Length: 153 amino acids
Theoretical weight: 17.04 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P46595 (Residues: 1-147; Coverage: 100%)
Gene names: SPBC119.02, ubc4
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 79 amino acids
Theoretical weight: 8.77 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CH07 (Residues: 1-75; Coverage: 59%)
Gene names: SPAC1805.12c, ubi2, uep1
Sequence domains: Ubiquitin family
E3 ubiquitin-protein ligase pub2 Chain: C
Molecule details ›
Chain: C
Length: 380 amino acids
Theoretical weight: 44.23 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UTG2 (Residues: 295-671; Coverage: 56%)
Gene names: SPAC1805.15c, pub2
Sequence domains: HECT-domain (ubiquitin-transferase)

Ligands and Environments

1 bound ligand:
Ligand A1AIV 1 x A1AIV
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.49Å
Relevant EMDB volumes: EMD-44204
Expression system: Escherichia coli BL21(DE3)

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