9JKB | pdb_00009jkb

Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquitin ligase complex.

Zhu, W.Chen, X.Zhang, J.Xu, C.

(2024) Biochem Biophys Res Commun 735: 150811-150811

  • DOI: https://doi.org/10.1016/j.bbrc.2024.150811
  • Primary Citation of Related Structures:  
    9JKB

  • PubMed Abstract: 

    Cullin-RING E3 ubiquitin ligases (CRLs) constitute the largest family of ubiquitin ligase and play important roles in regulation of proteostasis. Here we presented the cryo-EM structure of CRL1 FBXO4 , a member of Cullin-1 E3 ligase. CRL1 FBXO4 adopts a homodimer architecture. Structural analysis revealed that in the CRL1 FBXO4 protomer, the substrate recognition subunit FBXO4 interacts both the adaptor protein SKP1, and the scaffold protein CUL1 via hydrophobic and electrostatic interactions. Two FBXO4 forms a domain-swapped dimer in the CRL1 FBXO4 structure, which constitutes the basis for the dimerization of CRL1 FBXO4 . Inspired by the cryo-EM density, we modeled the architecture of whole CRL1 FBXO4 as a symmetrical dimer, which provides insights into CRL1 FBXO4 -medaited turnover of oncogene proteins.


  • Organizational Affiliation
    • MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Laboratory for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027, Hefei, PR China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
F-box only protein 4A [auth C],
E [auth D]
315Homo sapiensMutation(s): 0 
Gene Names: FBXO4FBX4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKT5 (Homo sapiens)
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Go to UniProtKB:  Q9UKT5
PHAROS:  Q9UKT5
GTEx:  ENSG00000151876 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKT5
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-1B [auth A]796Homo sapiensMutation(s): 0 
Gene Names: CUL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13616 (Homo sapiens)
Explore Q13616 
Go to UniProtKB:  Q13616
PHAROS:  Q13616
GTEx:  ENSG00000055130 
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UniProt GroupQ13616
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1C [auth B]166Homo sapiensMutation(s): 0 
Gene Names: SKP1EMC19OCP2SKP1ATCEB1L
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Find proteins for P63208 (Homo sapiens)
Explore P63208 
Go to UniProtKB:  P63208
PHAROS:  P63208
GTEx:  ENSG00000113558 
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UniProt GroupP63208
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1, N-terminally processedD [auth R]96Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.32 (UniProt), 2.3.2.27 (UniProt)
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Find proteins for P62877 (Homo sapiens)
Explore P62877 
Go to UniProtKB:  P62877
PHAROS:  P62877
GTEx:  ENSG00000100387 
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UniProt GroupP62877
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-10-23 
  • Deposition Author(s): Zhu, W., Xu, C.

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

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-23
    Changes: Data collection