5JIH

Crystal structure of HER2 binding IgG1-Fc (Fcab STAB19)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.663 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ig gamma-1 chain C region
A, B
227Homo sapiensMutation(s): 10 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Go to UniProtKB:  P01857
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.663 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.657α = 90.00
b = 79.465β = 90.00
c = 140.503γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHENIXphasing
EDNAdata collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references
  • Version 1.2: 2017-06-14
    Type: Database references