8G4Y

Structure of ZNRF3 ECD bound to peptide MK1-3.6.10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Potent and selective binders of the E3 ubiquitin ligase ZNRF3 stimulate Wnt signaling and intestinal organoid growth.

Kschonsak, Y.T.Gao, X.Miller, S.E.Hwang, S.Marei, H.Wu, P.Li, Y.Ruiz, K.Dorighi, K.Holokai, L.Perampalam, P.Tsai, W.K.Kee, Y.S.Agard, N.J.Harris, S.F.Hannoush, R.N.de Sousa E Melo, F.

(2024) Cell Chem Biol 31: 1176

  • DOI: https://doi.org/10.1016/j.chembiol.2023.11.006
  • Primary Citation of Related Structures:  
    8G4Y

  • PubMed Abstract: 

    Selective and precise activation of signaling transduction cascades is key for cellular reprogramming and tissue regeneration. However, the development of small- or large-molecule agonists for many signaling pathways has remained elusive and is rate limiting to realize the full clinical potential of regenerative medicine. Focusing on the Wnt pathway, here we describe a series of disulfide-constrained peptides (DCPs) that promote Wnt signaling activity by modulating the cell surface levels of ZNRF3, an E3 ubiquitin ligase that controls the abundance of the Wnt receptor complex FZD/LRP at the plasma membrane. Mechanistically, monomeric DCPs induce ZNRF3 ubiquitination, leading to its cell surface clearance, ultimately resulting in FZD stabilization. Furthermore, we engineered multimeric DCPs that induce expansive growth of human intestinal organoids, revealing a dependence between valency and ZNRF3 clearance. Our work highlights a strategy for the development of potent, biologically active Wnt signaling pathway agonists via targeting of ZNRF3.


  • Organizational Affiliation

    Department of Discovery Oncology, Genentech Inc, South San Francisco, CA 94080, USA. Electronic address: kschonsy@gene.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase ZNRF3178Homo sapiensMutation(s): 0 
Gene Names: ZNRF3KIAA1133RNF203
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULT6 (Homo sapiens)
Explore Q9ULT6 
Go to UniProtKB:  Q9ULT6
PHAROS:  Q9ULT6
GTEx:  ENSG00000183579 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULT6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MK1-3.6.1039synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.551α = 90
b = 35.226β = 109.11
c = 48.856γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Structure summary