8H3F

Cryo-EM Structure of the KBTBD2-CRL3-CSN complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.73 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

Dynamic molecular architecture and substrate recruitment of cullin3-RING E3 ligase CRL3 KBTBD2.

Hu, Y.Zhang, Z.Mao, Q.Zhang, X.Hao, A.Xun, Y.Wang, Y.Han, L.Zhan, W.Liu, Q.Yin, Y.Peng, C.Moresco, E.M.Y.Chen, Z.Beutler, B.Sun, L.

(2024) Nat Struct Mol Biol 31: 336-350

  • DOI: https://doi.org/10.1038/s41594-023-01182-6
  • Primary Citation of Related Structures:  
    8GQ6, 8H33, 8H34, 8H35, 8H36, 8H37, 8H38, 8H3A, 8H3F, 8H3Q, 8H3R

  • PubMed Abstract: 

    Phosphatidylinositol 3-kinase α, a heterodimer of catalytic p110α and one of five regulatory subunits, mediates insulin- and insulin like growth factor-signaling and, frequently, oncogenesis. Cellular levels of the regulatory p85α subunit are tightly controlled by regulated proteasomal degradation. In adipose tissue and growth plates, failure of K48-linked p85α ubiquitination causes diabetes, lipodystrophy and dwarfism in mice, as in humans with SHORT syndrome. Here we elucidated the structures of the key ubiquitin ligase complexes regulating p85α availability. Specificity is provided by the substrate receptor KBTBD2, which recruits p85α to the cullin3-RING E3 ubiquitin ligase (CRL3). CRL3 KBTBD2 forms multimers, which disassemble into dimers upon substrate binding (CRL3 KBTBD2 -p85α) and/or neddylation by the activator NEDD8 (CRL3 KBTBD2 ~N8), leading to p85α ubiquitination and degradation. Deactivation involves dissociation of NEDD8 mediated by the COP9 signalosome and displacement of KBTBD2 by the inhibitor CAND1. The hereby identified structural basis of p85α regulation opens the way to better understanding disturbances of glucose regulation, growth and cancer.


  • Organizational Affiliation

    Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 5A [auth E]334Homo sapiensMutation(s): 0 
Gene Names: COPS5CSN5JAB
EC: 3.4
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Find proteins for Q92905 (Homo sapiens)
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PHAROS:  Q92905
GTEx:  ENSG00000121022 
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UniProt GroupQ92905
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 1B [auth A]527Homo sapiensMutation(s): 0 
Gene Names: GPS1COPS1CSN1
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Find proteins for Q13098 (Homo sapiens)
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PHAROS:  Q13098
GTEx:  ENSG00000169727 
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UniProt GroupQ13098
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 2C [auth B]443Homo sapiensMutation(s): 0 
Gene Names: COPS2CSN2TRIP15
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PHAROS:  P61201
GTEx:  ENSG00000166200 
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UniProt GroupP61201
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 3D [auth C]441Homo sapiensMutation(s): 0 
Gene Names: COPS3CSN3
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Find proteins for Q9UNS2 (Homo sapiens)
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PHAROS:  Q9UNS2
GTEx:  ENSG00000141030 
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UniProt GroupQ9UNS2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 4E [auth D]406Homo sapiensMutation(s): 0 
Gene Names: COPS4CSN4
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PHAROS:  Q9BT78
GTEx:  ENSG00000138663 
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UniProt GroupQ9BT78
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 6327Homo sapiensMutation(s): 0 
Gene Names: COPS6CSN6HVIP
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PHAROS:  Q7L5N1
GTEx:  ENSG00000168090 
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UniProt GroupQ7L5N1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 7b220Homo sapiensMutation(s): 0 
Gene Names: COPS7BCSN7B
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GTEx:  ENSG00000144524 
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UniProt GroupQ9H9Q2
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 8209Homo sapiensMutation(s): 0 
Gene Names: COPS8CSN8
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GTEx:  ENSG00000198612 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch repeat and BTB domain-containing protein 2I,
K [auth M]
636Homo sapiensMutation(s): 1 
Gene Names: KBTBD2BKLHD1KIAA1489CGI-73
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Find proteins for Q8IY47 (Homo sapiens)
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GTEx:  ENSG00000170852 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1J [auth R]121Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
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GTEx:  ENSG00000100387 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-3768Homo sapiensMutation(s): 0 
Gene Names: CUL3KIAA0617
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GTEx:  ENSG00000036257 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81900729

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references