8Y1U | pdb_00008y1u

Crystal structure of ASB7-Elongin B/C bound to the LZTS1-degron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 
    0.243 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Molecular insights into degron recognition by CRL5 ASB7 ubiquitin ligase.

Zhou, M.Wang, X.Li, J.Ma, J.Bao, Z.Yan, X.Zhang, B.Liu, T.Yu, Y.Mi, W.Dong, C.

(2024) Nat Commun 15: 6177-6177

  • DOI: https://doi.org/10.1038/s41467-024-50556-x
  • Primary Citation of Related Structures:  
    8Y1U

  • PubMed Abstract: 

    The ankyrin (ANK) SOCS box (ASB) family, encompassing ASB1-18, is the largest group of substrate receptors of cullin 5 Ring E3 ubiquitin ligase. Nonetheless, the mechanism of substrate recognition by ASB family proteins has remained largely elusive. Here we present the crystal structure of ASB7-Elongin B-Elongin C ternary complex bound to a conserved helical degron. ASB7 employs its ANK3-6 to form an extended groove, effectively interacting with the internal α-helix-degron through a network of side-chain-mediated electrostatic and hydrophobic interactions. Our structural findings, combined with biochemical and cellular analyses, identify the key residues of the degron motif and ASB7 required for their recognition. This will facilitate the identification of additional physiological substrates of ASB7 by providing a defined degron motif for screening. Furthermore, the structural insights provide a basis for the rational design of compounds that can specifically target ASB7 by disrupting its interaction with its cognate degron.


  • Organizational Affiliation
    • The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ankyrin repeat and SOCS box protein 7309Homo sapiensMutation(s): 0 
Gene Names: ASB7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H672 (Homo sapiens)
Explore Q9H672 
Go to UniProtKB:  Q9H672
PHAROS:  Q9H672
GTEx:  ENSG00000183475 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H672
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide from Leucine zipper putative tumor suppressor 123Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y250 (Homo sapiens)
Explore Q9Y250 
Go to UniProtKB:  Q9Y250
PHAROS:  Q9Y250
GTEx:  ENSG00000061337 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y250
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-B104Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
PHAROS:  Q15370
GTEx:  ENSG00000103363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15370
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-C96Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
PHAROS:  Q15369
GTEx:  ENSG00000154582 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15369
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free:  0.243 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.145α = 90
b = 43.724β = 92
c = 159.233γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31900865
National Natural Science Foundation of China (NSFC)China32271265
National Natural Science Foundation of China (NSFC)China32071193

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release