4C84 | pdb_00004c84

zebrafish ZNRF3 ectodomain crystal form I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.259 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.222 (Depositor) 
  • R-Value Observed: 
    0.223 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4C84

This is version 1.2 of the entry. See complete history

Literature

Structural and Molecular Basis of Znrf3/Rnf43 Transmembrane Ubiquitin Ligase Inhibition by the Wnt Agonist R-Spondin.

Zebisch, M.Xu, Y.Krastev, C.Macdonald, B.T.Chen, M.Gilbert, R.J.C.He, X.Jones, E.Y.

(2013) Nat Commun 4: 2787

  • DOI: https://doi.org/10.1038/ncomms3787
  • Primary Citation Related Structures: 
    4C84, 4C85, 4C86, 4C8A, 4C8C, 4C8F, 4C8P, 4C8T, 4C8U, 4C8V, 4C8W, 4C99, 4C9A, 4C9E, 4C9R, 4C9U, 4C9V

  • PubMed Abstract: 

    The four R-spondin (Rspo) proteins are secreted agonists of Wnt signalling in vertebrates, functioning in embryogenesis and adult stem cell biology. Through ubiquitination and degradation of Wnt receptors, the transmembrane E3 ubiquitin ligase ZNRF3 and related RNF43 antagonize Wnt signalling. Rspo ligands have been reported to inhibit the ligase activity through direct interaction with ZNRF3 and RNF43. Here we report multiple crystal structures of the ZNRF3 ectodomain (ZNRF3(ecto)), a signalling-competent Furin1-Furin2 (Fu1-Fu2) fragment of Rspo2 (Rspo2(Fu1-Fu2)), and Rspo2(Fu1-Fu2) in complex with ZNRF3(ecto), or RNF43(ecto). A prominent loop in Fu1 clamps into equivalent grooves in the ZNRF3(ecto) and RNF43(ecto) surface. Rspo binding enhances dimerization of ZNRF3(ecto) but not of RNF43(ecto). Comparison of the four Rspo proteins, mutants and chimeras in biophysical and cellular assays shows that their signalling potency depends on their ability to recruit ZNRF3 or RNF43 via Fu1 into a complex with LGR receptors, which interact with Rspo via Fu2.


  • Organizational Affiliation
    • Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.

Macromolecule Content 

  • Total Structure Weight: 36.31 kDa 
  • Atom Count: 2,200 
  • Modeled Residue Count: 277 
  • Deposited Residue Count: 328 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
A, B
164Danio rerioMutation(s): 0 
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt
Find proteins for A5WWA0 (Danio rerio)
Explore A5WWA0 
Go to UniProtKB:  A5WWA0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5WWA0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.259 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.222 (Depositor) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.948α = 90
b = 53.296β = 102.1
c = 72.459γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2013-11-27
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Other, Structure summary