9KBD

Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-10-30 Released: 2025-02-19 
  • Deposition Author(s): Wei, J., Xu, C.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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

Structural Insight Into the SKP1-CUL1-FBXO3-RBX1 Complex.

Wei, J.Xu, C.

(2025) Proteins 

  • DOI: https://doi.org/10.1002/prot.26809
  • Primary Citation of Related Structures:  
    9KBD, 9KBF

  • PubMed Abstract: 

    The cryo-EM structure of human SCF FBXO3 , which consists of CUL1, RBX1, SKP1 and FBXO3 was solved at a nominal resolution of 3.70 Å. Although a previous study reported the crystal structure of the FBXO3 ApaG domain, how FBXO3 is incorporated into the SCF complex remains elusive. In the cryo-EM structure of SCF FBXO3 , the F-box domain of FBXO3 primarily associates with SKP1 via extensive hydrophobic interactions and interacts with the N-terminal region of CUL1 via hydrophobic interactions. The weak cryo-EM map of the RBX1 globular region is close to the FBXO3 ApaG domain, suggesting that unmodified SCF FBXO3 exhibits a closed conformation and that CUL1 neddylation is likely required to achieve high E3 activity. The structural study provides insight into the assembly of SCF FBXO3 and its activation mediated by CUL1 neddylation.


  • Organizational Affiliation

    MOE Key Laboratory for Membraneless Organelles and 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, Hefei, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1A [auth B]163Homo sapiensMutation(s): 0 
Gene Names: SKP1EMC19OCP2SKP1ATCEB1L
UniProt & NIH Common Fund Data Resources
Find proteins for P63208 (Homo sapiens)
Explore P63208 
Go to UniProtKB:  P63208
PHAROS:  P63208
GTEx:  ENSG00000113558 
Entity Groups  
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UniProt GroupP63208
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
F-box only protein 3B [auth C]436Homo sapiensMutation(s): 0 
Gene Names: FBXO3FBX3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UK99 (Homo sapiens)
Explore Q9UK99 
Go to UniProtKB:  Q9UK99
PHAROS:  Q9UK99
GTEx:  ENSG00000110429 
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UniProt GroupQ9UK99
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1C [auth R]108Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
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
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-1D [auth A]776Homo 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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-02-19 
  • Deposition Author(s): Wei, J., Xu, C.

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

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Data collection, Database references