6O39

Crystal structure of Frizzled 5 CRD in complex with F2.I Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1073/pnas.1817246116
  • Structures With Same Primary Citation

  • 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 ...

    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

    Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antibody F2.I Fab, Light chainA213Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antibody F2.I Fab, Heavy chainB221Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Frizzled-5C123Homo sapiensMutation(s): 0 
Gene Names: FZD5C2orf31
Find proteins for Q13467 (Homo sapiens)
Explore Q13467 
Go to UniProtKB:  Q13467
NIH Common Fund Data Resources
PHAROS  Q13467
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B, C
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.405α = 90
b = 101.405β = 90
c = 196.497γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XPREPdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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