3MZW

HER2 extracelluar region with affinity matured 3-helix affibody ZHER2:342


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for high-affinity HER2 receptor binding by an engineered protein.

Eigenbrot, C.Ultsch, M.Dubnovitsky, A.Abrahmsen, L.Hard, T.

(2010) Proc.Natl.Acad.Sci.USA 107: 15039-15044

  • DOI: 10.1073/pnas.1005025107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human epidermal growth factor receptor 2 (HER2) is specifically overexpressed in tumors of several cancers, including an aggressive form of breast cancer. It is therefore a target for both cancer diagnostics and therapy. The 58 amino acid residue ...

    The human epidermal growth factor receptor 2 (HER2) is specifically overexpressed in tumors of several cancers, including an aggressive form of breast cancer. It is therefore a target for both cancer diagnostics and therapy. The 58 amino acid residue Zher2 affibody molecule was previously engineered as a high-affinity binder of HER2. Here we determined the structure of Zher2 in solution and the crystal structure of Zher2 in complex with the HER2 extracellular domain. Zher2 binds to a conformational epitope on HER2 that is distant from those recognized by the therapeutic antibodies trastuzumab and pertuzumab. Its small size and lack of interference may provide Zher2 with advantages for diagnostic use or even for delivery of therapeutic agents to HER2-expressing tumors when trastuzumab or pertuzumab are already employed. Biophysical characterization shows that Zher2 is thermodynamically stable in the folded state yet undergoing conformational interconversion on a submillisecond time scale. The data suggest that it is the HER2-binding conformation that is formed transiently prior to binding. Still, binding is very strong with a dissociation constant K(D) = 22 pM, and perfect conformational homogeneity is therefore not necessarily required in engineered binding proteins. A comparison of the original Z domain scaffold to free and bound Zher2 structures reveals how high-affinity binding has evolved during selection and affinity maturation and suggests how a compromise between binding surface optimization and stability and dynamics of the unbound state has been reached.


    Organizational Affiliation

    Department of Structural Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA. eigenbrot.c@gene.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine kinase-type cell surface receptor HER2
A
624Homo sapiensMutation(s): 0 
Gene Names: ERBB2 (HER2, MLN19, NEU, NGL)
EC: 2.7.10.1
Find proteins for P04626 (Homo sapiens)
Go to Gene View: ERBB2
Go to UniProtKB:  P04626
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin G-binding protein A
B
58Staphylococcus aureusMutation(s): 14 
Gene Names: spa
Find proteins for P38507 (Staphylococcus aureus)
Go to UniProtKB:  P38507
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.726α = 90.00
b = 97.841β = 90.00
c = 148.283γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Derived calculations, Refinement description