8KHP

CULLIN3-KLHL22-RBX1 E3 ligase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM structure of the KLHL22 E3 ligase bound to an oligomeric metabolic enzyme.

Teng, F.Wang, Y.Liu, M.Tian, S.Stjepanovic, G.Su, M.Y.

(2023) Structure 31: 1431-1440.e5

  • DOI: https://doi.org/10.1016/j.str.2023.09.002
  • Primary Citation of Related Structures:  
    8KGY, 8KHP, 8W4J

  • PubMed Abstract: 

    CULLIN-RING ligases constitute the largest group of E3 ubiquitin ligases. While some CULLIN family members recruit adapters before engaging further with different substrate receptors, homo-dimeric BTB-Kelch family proteins combine adapter and substrate receptor into a single polypeptide for the CULLIN3 family. However, the entire structural assembly and molecular details have not been elucidated to date. Here, we present a cryo-EM structure of the CULLIN3 RBX1 in complex with Kelch-like protein 22 (KLHL22) and a mitochondrial glutamate dehydrogenase complex I (GDH1) at 3.06 Å resolution. The structure adopts a W-shaped architecture formed by E3 ligase dimers. Three CULLIN3 KLHL22-RBX1 dimers were found to be dynamically associated with a single GDH1 hexamer. CULLIN3 KLHL22-RBX1 ligase mediated the polyubiquitination of GDH1 in vitro. Together, these results enabled the establishment of a structural model for understanding the complete assembly of BTB-Kelch proteins with CULLIN3 and how together they recognize oligomeric substrates and target them for ubiquitination.


  • Organizational Affiliation

    Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch-like protein 22
A, B
634Homo sapiensMutation(s): 0 
Gene Names: KLHL22
UniProt & NIH Common Fund Data Resources
Find proteins for Q53GT1 (Homo sapiens)
Explore Q53GT1 
Go to UniProtKB:  Q53GT1
PHAROS:  Q53GT1
GTEx:  ENSG00000099910 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53GT1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-3
C, D
768Homo sapiensMutation(s): 0 
Gene Names: CUL3KIAA0617
UniProt & NIH Common Fund Data Resources
Find proteins for Q13618 (Homo sapiens)
Explore Q13618 
Go to UniProtKB:  Q13618
PHAROS:  Q13618
GTEx:  ENSG00000036257 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13618
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1
E, F
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62877
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina2022A1515010856

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release