› 8wqc

Electron Microscopy
3.54Å resolution

cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CDK5R1

Released:
DOI: 10.2210/pdb8wqc/pdb
PDB entry 8wqc coloured by chain, front view.
PDB entry 8wqc coloured by chain, side view.
PDB entry 8wqc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of Ψ-Pro/C-degron recognition by the CRL2FEM1B ubiquitin ligase.
Chen X, Raiff A, Li S, Guo Q, Zhang J, Zhou H, Timms RT, Yao X, Elledge SJ, Koren I, Zhang K, Xu C
OpenAccess logo Nat Commun 15 3558 (2024)
PMID: 38670995
Related structures: EMD-37739

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
S-[NEDD8-protein]-yl-[E2 NEDD8-conjugating enzyme]-L-cysteine + [cullin]-L-lysine = [E2 NEDD8-conjugating enzyme]-L-cysteine + N(6)-[NEDD8-protein]-yl-[cullin]-L-lysine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-242606 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
Elongin-B Chains: D, I
Molecule details ›
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
Sequence domains: Ubiquitin family
E3 ubiquitin-protein ligase RBX1, N-terminally processed Chains: F, J
Molecule details ›
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
Sequence domains: RING-H2 zinc finger domain
Elongin-C Chains: B, H
Molecule details ›
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
Sequence domains: Skp1 family, tetramerisation domain
Cullin-2 Chains: C, E
Molecule details ›
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
Sequence domains:
NEDD8 Chains: K, N
Molecule details ›
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
Sequence domains: Ubiquitin family
Protein fem-1 homolog B Chains: A, G
Molecule details ›
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
Sequence domains: Ankyrin repeats (3 copies)

Ligands and Environments

1 bound ligand:
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.54Å
Relevant EMDB volumes: EMD-37739
Expression system: Escherichia coli

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