8WQC image
Entry Detail
PDB ID:
8WQC
EMDB ID:
Keywords:
Title:
cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CDK5R1
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2023-10-11
Release Date:
2024-04-03
Method Details:
Experimental Method:
Resolution:
3.54 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Protein fem-1 homolog B
Chain IDs:K (auth: A), L (auth: G)
Chain Length:627
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Elongin-C
Chain IDs:C (auth: B), H
Chain Length:96
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Cullin-2
Chain IDs:D (auth: C), F (auth: E)
Chain Length:750
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Elongin-B
Chain IDs:A (auth: D), I
Chain Length:118
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:E3 ubiquitin-protein ligase RBX1, N-terminally processed
Chain IDs:B (auth: F), E (auth: J)
Chain Length:96
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:NEDD8
Chain IDs:G (auth: N), J (auth: K)
Chain Length:76
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Mechanism of Psi-Pro/C-degron recognition by the CRL2 FEM1B ubiquitin ligase.
Nat Commun 15 3558 3558 (2024)
PMID: 38670995 DOI: 10.1038/s41467-024-47890-5

Abstact

The E3 ligase-degron interaction determines the specificity of the ubiquitin‒proteasome system. We recently discovered that FEM1B, a substrate receptor of Cullin 2-RING ligase (CRL2), recognizes C-degrons containing a C-terminal proline. By solving several cryo-EM structures of CRL2FEM1B bound to different C-degrons, we elucidate the dimeric assembly of the complex. Furthermore, we reveal distinct dimerization states of unmodified and neddylated CRL2FEM1B to uncover the NEDD8-mediated activation mechanism of CRL2FEM1B. Our research also indicates that, FEM1B utilizes a bipartite mechanism to recognize both the C-terminal proline and an upstream aromatic residue within the substrate. These structural findings, complemented by in vitro ubiquitination and in vivo cell-based assays, demonstrate that CRL2FEM1B-mediated polyubiquitination and subsequent protein turnover depend on both FEM1B-degron interactions and the dimerization state of the E3 ligase complex. Overall, this study deepens our molecular understanding of how Cullin-RING E3 ligase substrate selection mediates protein turnover.

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Primary Citation of related structures