8FFJ | pdb_00008ffj

Structure of Zanidatamab bound to HER2

• PDB DOI: https://doi.org/10.2210/pdb8FFJ/pdb
• EM Map EMD-29044: EMDB EMDataResource

• Classification: TRANSFERASE/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2022-12-08 Released: 2023-02-22 
• Deposition Author(s): Worrall, L.J., Atkinson, C.E., Sanches, M., Dixit, S., Strynadka, N.C.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

An anti-HER2 biparatopic antibody that induces unique HER2 clustering and complement-dependent cytotoxicity.

Weisser, N.E., Sanches, M., Escobar-Cabrera, E., O'Toole, J., Whalen, E., Chan, P.W.Y., Wickman, G., Abraham, L., Choi, K., Harbourne, B., Samiotakis, A., Rojas, A.H., Volkers, G., Wong, J., Atkinson, C.E., Baardsnes, J., Worrall, L.J., Browman, D., Smith, E.E., Baichoo, P., Cheng, C.W., Guedia, J., Kang, S., Mukhopadhyay, A., Newhook, L., Ohrn, A., Raghunatha, P., Zago-Schmitt, M., Schrag, J.D., Smith, J., Zwierzchowski, P., Scurll, J.M., Fung, V., Black, S., Strynadka, N.C.J., Gold, M.R., Presta, L.G., Ng, G., Dixit, S.

(2023) Nat Commun 14: 1394-1394

• PubMed: 36914633 
• DOI: https://doi.org/10.1038/s41467-023-37029-3
• Primary Citation Related Structures: 
  8FFJ


• PubMed Abstract: 
  

  Human epidermal growth factor receptor 2 (HER2) is a receptor tyrosine kinase that plays an oncogenic role in breast, gastric and other solid tumors. However, anti-HER2 therapies are only currently approved for the treatment of breast and gastric/gastric esophageal junction cancers and treatment resistance remains a problem. Here, we engineer an anti-HER2 IgG1 bispecific, biparatopic antibody (Ab), zanidatamab, with unique and enhanced functionalities compared to both trastuzumab and the combination of trastuzumab plus pertuzumab (tras + pert). Zanidatamab binds adjacent HER2 molecules in trans and initiates distinct HER2 reorganization, as shown by polarized cell surface HER2 caps and large HER2 clusters, not observed with trastuzumab or tras + pert. Moreover, zanidatamab, but not trastuzumab nor tras + pert, elicit potent complement-dependent cytotoxicity (CDC) against high HER2-expressing tumor cells in vitro. Zanidatamab also mediates HER2 internalization and downregulation, inhibition of both cell signaling and tumor growth, antibody-dependent cellular cytotoxicity (ADCC) and phagocytosis (ADCP), and also shows superior in vivo antitumor activity compared to tras + pert in a HER2-expressing xenograft model. Collectively, we show that zanidatamab has multiple and distinct mechanisms of action derived from the structural effects of biparatopic HER2 engagement.

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Organizational Affiliation: 
• Zymeworks BC Inc., 114 East 4th Avenue, Suite 800, Vancouver, BC, Canada. [e-mail].
Zymeworks BC Inc., 114 East 4th Avenue, Suite 800, Vancouver, BC, Canada.
Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada.
HRMEM Facility, University of British Columbia, Vancouver, BC, Canada.
Human Health Therapeutics Portfolio, NRC-CNRC, Montreal, QC, Canada.
Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada.
Department of Urologic Sciences (Vancouver Prostate Centre) and the Institute of Applied Mathematics, University of British Columbia, Vancouver, BC, Canada.
AbbVie, 1N. Waukegan Road, North Chicago, IL, 60064, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 194.04 kDa 
• Atom Count: 8,968 
• Modeled Residue Count: 1,170 
• Deposited Residue Count: 1,773 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	A [auth X]	622	Homo sapiens	Mutation(s): 0  Gene Names: ERBB2, HER2, MLN19, NEU, NGL EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens) Explore P04626  Go to UniProtKB:  P04626
PHAROS:  P04626 GTEx:  ENSG00000141736

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Zanidatamab Heavy Chain A	B [auth J]	451	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Zanidatamab Light Chain A	C [auth Q]	217	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Zanidatamab Heavy Chain B	D [auth I]	483	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Worrall, L.J., Atkinson, C.E., Sanches, M., Dixit, S., Strynadka, N.C.J.

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Funding Organization	Location	Grant Number
Not funded	Canada	--

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2024-09-04
  Changes: Data collection, Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary