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cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 1)

Electron Microscopy
4.09Å resolution
PDB entry 8wqg coloured by chain, front view.
PDB entry 8wqg coloured by chain, side view.
PDB entry 8wqg coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero dodecamer (preferred)
Entry contents: 6 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero dodecamer
Accessible surface area: 151270.94 Å2
Buried surface area: 29606.33 Å2
Dissociation area: 947.36 Å2
Dissociation energy (ΔGdiss): 2.4 kcal/mol
Dissociation entropy (TΔSdiss): 10.89 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-274098

Macromolecules

Elongin-B
Chains: D, I
Length: 118 amino acids
Theoretical weight: 13.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15370 (Residues: 1-118; Coverage: 100%)
Gene names: ELOB, TCEB2
Pfam: Ubiquitin family
Elongin-B in PDB entry 8wqg, assembly 1, front view.
Elongin-B in PDB entry 8wqg, assembly 1, side view.
Elongin-B in PDB entry 8wqg, assembly 1, top view.
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E3 ubiquitin-protein ligase RBX1, N-terminally processed
Chains: F, J
Length: 96 amino acids
Theoretical weight: 11.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62877 (Residues: 16-108; Coverage: 86%)
Gene names: RBX1, RNF75, ROC1
Pfam: RING-H2 zinc finger domain
E3 ubiquitin-protein ligase RBX1, N-terminally processed in PDB entry 8wqg, assembly 1, front view.
E3 ubiquitin-protein ligase RBX1, N-terminally processed in PDB entry 8wqg, assembly 1, side view.
E3 ubiquitin-protein ligase RBX1, N-terminally processed in PDB entry 8wqg, assembly 1, top view.
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Elongin-C
Chains: B, H
Length: 96 amino acids
Theoretical weight: 10.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15369 (Residues: 17-112; Coverage: 86%)
Gene names: ELOC, TCEB1
Pfam: Skp1 family, tetramerisation domain
Elongin-C in PDB entry 8wqg, assembly 1, front view.
Elongin-C in PDB entry 8wqg, assembly 1, side view.
Elongin-C in PDB entry 8wqg, assembly 1, top view.
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Cullin-2
Chains: C, E
Length: 750 amino acids
Theoretical weight: 87.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13617 (Residues: 2-745; Coverage: 98%)
Gene name: CUL2
Pfam:
Cullin-2 in PDB entry 8wqg, assembly 1, front view.
Cullin-2 in PDB entry 8wqg, assembly 1, side view.
Cullin-2 in PDB entry 8wqg, assembly 1, top view.
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Ubiquitin-like protein NEDD8
Chains: K, N
Length: 76 amino acids
Theoretical weight: 8.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15843 (Residues: 1-76; Coverage: 94%)
Gene name: NEDD8
Pfam: Ubiquitin family
NEDD8 in PDB entry 8wqg, assembly 1, front view.
NEDD8 in PDB entry 8wqg, assembly 1, side view.
NEDD8 in PDB entry 8wqg, assembly 1, top view.
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Protein fem-1 homolog B
Chains: A, G
Length: 627 amino acids
Theoretical weight: 70.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UK73 (Residues: 1-627; Coverage: 100%)
Gene names: F1AA, FEM1B, KIAA0396
Pfam: Ankyrin repeats (3 copies)
Protein fem-1 homolog B in PDB entry 8wqg, assembly 1, front view.
Protein fem-1 homolog B in PDB entry 8wqg, assembly 1, side view.
Protein fem-1 homolog B in PDB entry 8wqg, assembly 1, top view.
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