6O3B

Crystal structure of Frizzled 7 CRD in complex with F6 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-guided design fine-tunes pharmacokinetics, tolerability, and antitumor profile of multispecific frizzled antibodies.

Raman, S.Beilschmidt, M.To, M.Lin, K.Lui, F.Jmeian, Y.Ng, M.Fernandez, M.Fu, Y.Mascall, K.Duque, A.Wang, X.Pan, G.Angers, S.Moffat, J.Sidhu, S.S.Magram, J.Sinclair, A.M.Fransson, J.Julien, J.P.

(2019) Proc Natl Acad Sci U S A 116: 6812-6817

  • DOI: https://doi.org/10.1073/pnas.1817246116
  • Primary Citation of Related Structures:  
    6O39, 6O3A, 6O3B

  • PubMed Abstract: 

    Aberrant activation of Wnt/β-catenin signaling occurs frequently in cancer. However, therapeutic targeting of this pathway is complicated by the role of Wnt in stem cell maintenance and tissue homeostasis. Here, we evaluated antibodies blocking 6 of the 10 human Wnt/Frizzled (FZD) receptors as potential therapeutics. Crystal structures revealed a common binding site for these monoclonal antibodies (mAbs) on FZD, blocking the interaction with the Wnt palmitoleic acid moiety. However, these mAbs displayed gastrointestinal toxicity or poor plasma exposure in vivo. Structure-guided engineering was used to refine the binding of each mAb for FZD receptors, resulting in antibody variants with improved in vivo tolerability and developability. Importantly, the lead variant mAb significantly inhibited tumor growth in the HPAF-II pancreatic tumor xenograft model. Taken together, our data demonstrate that anti-FZD cancer therapeutic antibodies with broad specificity can be fine-tuned to navigate in vivo exposure and tolerability while driving therapeutic efficacy.


  • Organizational Affiliation

    Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody Fab F6, Light chainA,
D [auth E]
214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody Fab F6, Heavy chainB,
E [auth G]
221Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Frizzled-7C,
F [auth H]
140Homo sapiensMutation(s): 0 
Gene Names: FZD7
UniProt & NIH Common Fund Data Resources
Find proteins for O75084 (Homo sapiens)
Explore O75084 
Go to UniProtKB:  O75084
PHAROS:  O75084
GTEx:  ENSG00000155760 
Entity Groups  
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UniProt GroupO75084
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.642α = 90
b = 85.848β = 95.82
c = 104.103γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XPREPdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary