5KWG

Crystal structure of extracellular domain of HER2 in complex with Fcab H10-03-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.324 
  • R-Value Observed: 0.328 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Fcab-HER2 Interaction: a Menage a Trois. Lessons from X-Ray and Solution Studies.

Lobner, E.Humm, A.S.Goritzer, K.Mlynek, G.Puchinger, M.G.Hasenhindl, C.Ruker, F.Traxlmayr, M.W.Djinovic-Carugo, K.Obinger, C.

(2017) Structure 25: 878-889.e5

  • DOI: 10.1016/j.str.2017.04.014
  • Primary Citation of Related Structures:  
    5JII, 5JIH, 5JIK, 5K33, 5KWG

  • PubMed Abstract: 
  • The crystallizable fragment (Fc) of the immunoglobulin class G (IgG) is an attractive scaffold for the design of novel therapeutics. Upon engineering the C-terminal loops in the CH3 domains, Fcabs (Fc domain with antigen-binding sites) can be designe ...

    The crystallizable fragment (Fc) of the immunoglobulin class G (IgG) is an attractive scaffold for the design of novel therapeutics. Upon engineering the C-terminal loops in the CH3 domains, Fcabs (Fc domain with antigen-binding sites) can be designed. We present the first crystal structures of Fcabs, i.e., of the HER2-binding clone H10-03-6 having the AB and EF loop engineered and the stabilized version STAB19 derived by directed evolution. Comparison with the crystal structure of the Fc wild-type protein reveals conservation of the overall domain structures but significant differences in EF-loop conformations. Furthermore, we present the first Fcab-antigen complex structures demonstrating the interaction between the engineered Fcab loops with domain IV of HER2. The crystal structures of the STAB19-HER2 and H10-03-6-HER2 complexes together with analyses by isothermal titration calorimetry, SEC-MALS, and fluorescence correlation spectroscopy show that one homodimeric Fcab binds two HER2 molecules following a negative cooperative binding behavior.


    Organizational Affiliation

    Christian Doppler Laboratory for Antibody Engineering, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; Department of Chemistry, Division of Biochemistry, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria. Electronic address: christian.obinger@boku.ac.at.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor tyrosine-protein kinase erbB-2C631Homo sapiensMutation(s): 0 
Gene Names: ERBB2HER2MLN19NEUNGL
EC: 2.7.10.1
Find proteins for P04626 (Homo sapiens)
Explore P04626 
Go to UniProtKB:  P04626
NIH Common Fund Data Resources
PHAROS  P04626
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ig gamma-1 chain C regionA228Homo sapiensMutation(s): 10 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Explore P01857 
Go to UniProtKB:  P01857
NIH Common Fund Data Resources
PHAROS  P01857
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.324 
  • R-Value Observed: 0.328 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.77α = 90
b = 109.77β = 90
c = 176.07γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
EDNAdata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Christian Doppler Research AssociationAustriaChristian Doppler Laboratory for Antibody Engineering
Austrian Science FundAustriaFWF W1224 (Doctoral Program on Biomolecular Technology of Proteins , BioToP)

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references
  • Version 1.2: 2017-06-14
    Changes: Database references
  • Version 1.3: 2017-08-16
    Changes: Data collection