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 8WQA | pdb_00008wqa

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

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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 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.

Macromolecule Content 

  • Total Structure Weight: 392.16 kDa 
  • Atom Count: 26,479 
  • Modeled Residue Count: 3,301 
  • Deposited Residue Count: 3,436 
  • Unique protein chains: 6

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
UniProt & NIH Common Fund Data Resources
Find proteins for Q13617 (Homo sapiens)
Explore Q13617 
Go to UniProtKB:  Q13617
PHAROS:  Q13617
GTEx:  ENSG00000108094 
Entity Groups
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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: FEM1B, F1AA, KIAA0396
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UK73 (Homo sapiens)
Explore Q9UK73 
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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: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
PHAROS:  Q15369
GTEx:  ENSG00000154582 
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UniProt GroupQ15369
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin-BD [auth F],
G [auth H]
118Homo sapiensMutation(s): 0 
Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
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PHAROS:  Q15370
GTEx:  ENSG00000103363 
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UniProt GroupQ15370
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Reference Sequence
Find similar proteins by:|  3D Structure
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: RBX1, RNF75, ROC1
EC: 2.3.2.32 (UniProt), 2.3.2.27 (UniProt)
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Find proteins for P62877 (Homo sapiens)
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PHAROS:  P62877
GTEx:  ENSG00000100387 
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UniProt GroupP62877
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 89
K, L
31Homo sapiensMutation(s): 0 
Gene Names: CCDC89, BOIP
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N998 (Homo sapiens)
Explore Q8N998 
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GTEx:  ENSG00000179071 
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UniProt GroupQ8N998
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Reference Sequence

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