8H33

Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 tetrameric complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.86 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kelch repeat and BTB domain-containing protein 2A,
B,
C [auth G],
D [auth J]
623Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IY47 (Homo sapiens)
Explore Q8IY47 
Go to UniProtKB:  Q8IY47
PHAROS:  Q8IY47
GTEx:  ENSG00000170852 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IY47
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1E [auth D],
H [auth K],
J [auth L],
L [auth E]
121Homo 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-3F,
G [auth H],
I,
K [auth C]
776Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13618 (Homo sapiens)
Explore Q13618 
Go to UniProtKB:  Q13618
PHAROS:  Q13618
GTEx:  ENSG00000036257 
Entity Groups  
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UniProt GroupQ13618
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
M [auth D]
N [auth D]
O [auth D]
P [auth K]
Q [auth K]
M [auth D],
N [auth D],
O [auth D],
P [auth K],
Q [auth K],
R [auth K],
S [auth L],
T [auth L],
U [auth L],
V [auth E],
W [auth E],
X [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.86 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