› 9b5m

Electron Microscopy
2.79Å resolution

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - consensus map and model

Released:
DOI: 10.2210/pdb9b5m/pdb
PDB entry 9b5m coloured by chain, front view.
PDB entry 9b5m coloured by chain, side view.
PDB entry 9b5m 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-44217

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:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-131720 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-activating enzyme E1 1 Chain: A
Molecule details ›
Chain: A
Length: 1001 amino acids
Theoretical weight: 111.76 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O94609 (Residues: 13-1012; Coverage: 99%)
Gene names: SPBC1604.21c, SPBC211.09, ptr3
Sequence domains:
Ubiquitin-conjugating enzyme E2 4 Chain: C
Molecule details ›
Chain: C
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: D
Molecule details ›
Chain: D
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

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand ATP 1 x ATP
Ligand A1AIV 1 x A1AIV
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.79Å
Relevant EMDB volumes: EMD-44217
Expression system: Escherichia coli BL21(DE3)

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