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

Electron Microscopy
2.5Å resolution
PDB entry 9b5c coloured by chain, front view.
PDB entry 9b5c coloured by chain, side view.
PDB entry 9b5c coloured by chain, top view.
Source organism: Schizosaccharomyces pombe 972h-
Assembly composition:
hetero tetramer (preferred)
Entry contents: 4 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero tetramer
Accessible surface area: 50389.86 Å2
Buried surface area: 7523.51 Å2
Dissociation area: 1,566.96 Å2
Dissociation energy (ΔGdiss): 5.94 kcal/mol
Dissociation entropy (TΔSdiss): 13.12 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-245041

Macromolecules

Ubiquitin-activating enzyme E1 1
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
Pfam:
Ubiquitin-activating enzyme E1 1 in PDB entry 9b5c, assembly 1, front view.
Ubiquitin-activating enzyme E1 1 in PDB entry 9b5c, assembly 1, side view.
Ubiquitin-activating enzyme E1 1 in PDB entry 9b5c, assembly 1, top view.
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Ubiquitin
Chain: B
Length: 76 amino acids
Theoretical weight: 8.57 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CH07 (Residues: 1-76; Coverage: 59%)
Gene names: SPAC1805.12c, ubi2, uep1
Pfam: Ubiquitin family
Large ribosomal subunit protein eL40B in PDB entry 9b5c, assembly 1, front view.
Large ribosomal subunit protein eL40B in PDB entry 9b5c, assembly 1, side view.
Large ribosomal subunit protein eL40B in PDB entry 9b5c, assembly 1, top view.
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Ubiquitin-conjugating enzyme E2 4
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
Pfam: Ubiquitin-conjugating enzyme
Ubiquitin-conjugating enzyme E2 4 in PDB entry 9b5c, assembly 1, front view.
Ubiquitin-conjugating enzyme E2 4 in PDB entry 9b5c, assembly 1, side view.
Ubiquitin-conjugating enzyme E2 4 in PDB entry 9b5c, assembly 1, top view.
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Ubiquitin
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
Pfam: Ubiquitin family
Ubiquitin in PDB entry 9b5c, assembly 1, front view.
Ubiquitin in PDB entry 9b5c, assembly 1, side view.
Ubiquitin in PDB entry 9b5c, assembly 1, top view.
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