8WQA

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of Psi-Pro/C-degron recognition by the CRL2 FEM1B ubiquitin ligase.

Chen, X.Raiff, A.Li, S.Guo, Q.Zhang, J.Zhou, H.Timms, R.T.Yao, X.Elledge, S.J.Koren, I.Zhang, K.Xu, C.

(2024) Nat Commun 15: 3558-3558

  • DOI: https://doi.org/10.1038/s41467-024-47890-5
  • Primary Citation of Related Structures:  
    8WQA, 8WQB, 8WQC, 8WQD, 8WQE, 8WQF, 8WQG, 8WQH, 8WQI

  • PubMed Abstract: 

    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 CRL2 FEM1B bound to different C-degrons, we elucidate the dimeric assembly of the complex. Furthermore, we reveal distinct dimerization states of unmodified and neddylated CRL2 FEM1B to uncover the NEDD8-mediated activation mechanism of CRL2 FEM1B . 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 CRL2 FEM1B -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.


  • Organizational Affiliation

    MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-2A [auth C],
I [auth A]
750Homo sapiensMutation(s): 0 
Gene Names: CUL2
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Find proteins for Q13617 (Homo sapiens)
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Go to UniProtKB:  Q13617
PHAROS:  Q13617
GTEx:  ENSG00000108094 
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UniProt GroupQ13617
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein fem-1 homolog BB [auth D],
J [auth B]
627Homo sapiensMutation(s): 0 
Gene Names: FEM1BF1AAKIAA0396
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Find proteins for Q9UK73 (Homo sapiens)
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PHAROS:  Q9UK73
GTEx:  ENSG00000169018 
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UniProt GroupQ9UK73
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-CC [auth E],
F [auth G]
96Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
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Find proteins for Q15369 (Homo sapiens)
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GTEx:  ENSG00000154582 
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UniProt GroupQ15369
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-BD [auth F],
G [auth H]
118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
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GTEx:  ENSG00000103363 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1, N-terminally processedE [auth J],
H [auth I]
96Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.32 (UniProt), 2.3.2.27 (UniProt)
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GTEx:  ENSG00000100387 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 89
K, L
31Homo sapiensMutation(s): 0 
Gene Names: CCDC89BOIP
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Find proteins for Q8N998 (Homo sapiens)
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GTEx:  ENSG00000179071 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references