3MZW image
Deposition Date 2010-05-13
Release Date 2010-07-28
Last Version Date 2024-10-30
Entry Detail
PDB ID:
3MZW
Keywords:
Title:
HER2 extracelluar region with affinity matured 3-helix affibody ZHER2:342
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.90 Å
R-Value Free:
0.27
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Tyrosine kinase-type cell surface receptor HER2
Gene (Uniprot):ERBB2
Chain IDs:A
Chain Length:624
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Immunoglobulin G-binding protein A
Gene (Uniprot):spa
Mutations:A212V, Q220M, Q221R, F224Y, Y225W, L228A, H229L, E235N, E236Q, R238K, N239R, G240A, Q243R, K246Y
Chain IDs:B
Chain Length:58
Number of Molecules:1
Biological Source:Staphylococcus aureus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN A ASN GLYCOSYLATION SITE
Ligand Molecules
Primary Citation
Structural basis for high-affinity HER2 receptor binding by an engineered protein.
Proc.Natl.Acad.Sci.USA 107 15039 15044 (2010)
PMID: 20696930 DOI: 10.1073/pnas.1005025107

Abstact

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.

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Primary Citation of related structures