4K3J

Crystal structure of Onartuzumab Fab in complex with MET and HGF-beta

• PDB DOI:  https://doi.org/10.2210/pdb4K3J/pdb

• Classification: Transferase/Immune System/Growth Factor
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-04-10 Released: 2013-08-28 
• Deposition Author(s): Ma, X., Starovasnik, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.253 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Literature

Monovalent antibody design and mechanism of action of onartuzumab, a MET antagonist with anti-tumor activity as a therapeutic agent.

Merchant, M., Ma, X., Maun, H.R., Zheng, Z., Peng, J., Romero, M., Huang, A., Yang, N.Y., Nishimura, M., Greve, J., Santell, L., Zhang, Y.W., Su, Y., Kaufman, D.W., Billeci, K.L., Mai, E., Moffat, B., Lim, A., Duenas, E.T., Phillips, H.S., Xiang, H., Young, J.C., Vande Woude, G.F., Dennis, M.S., Reilly, D.E., Schwall, R.H., Starovasnik, M.A., Lazarus, R.A., Yansura, D.G.

(2013) Proc Natl Acad Sci U S A 110: E2987-E2996

• PubMed: 23882082 
• DOI: https://doi.org/10.1073/pnas.1302725110
• Primary Citation of Related Structures:  
  4K3J


• PubMed Abstract: 
  

Binding of hepatocyte growth factor (HGF) to the receptor tyrosine kinase MET is implicated in the malignant process of multiple cancers, making disruption of this interaction a promising therapeutic strategy. However, targeting MET with bivalent antibodies can mimic HGF agonism via receptor dimerization. To address this limitation, we have developed onartuzumab, an Escherichia coli-derived, humanized, and affinity-matured monovalent monoclonal antibody against MET, generated using the knob-into-hole technology that enables the antibody to engage the receptor in a one-to-one fashion. Onartuzumab potently inhibits HGF binding and receptor phosphorylation and signaling and has antibody-like pharmacokinetics and antitumor activity. Biochemical data and a crystal structure of a ternary complex of onartuzumab antigen-binding fragment bound to a MET extracellular domain fragment, consisting of the MET Sema domain fused to the adjacent Plexins, Semaphorins, Integrins domain (MET Sema-PSI), and the HGF β-chain demonstrate that onartuzumab acts specifically by blocking HGF α-chain (but not β-chain) binding to MET. These data suggest a likely binding site of the HGF α-chain on MET, which when dimerized leads to MET signaling. Onartuzumab, therefore, represents the founding member of a class of therapeutic monovalent antibodies that overcomes limitations of antibody bivalency for targets impacted by antibody crosslinking.

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Organizational Affiliation: 

Department of Translational Oncology, Genentech, Inc., South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 135.38 kDa 
• Atom Count: 9,281 
• Modelled Residue Count: 1,164 
• Deposited Residue Count: 1,211 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor	A	233	Homo sapiens	Mutation(s): 1  Gene Names: HGF, HPTA
UniProt & NIH Common Fund Data Resources
Find proteins for P14210 (Homo sapiens) Explore P14210  Go to UniProtKB:  P14210
PHAROS:  P14210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor beta chain	B	534	Homo sapiens	Mutation(s): 0  Gene Names: MET EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens) Explore P08581  Go to UniProtKB:  P08581
PHAROS:  P08581

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Onartuzumab Fab heavy chain	C [auth H]	224	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Onartuzumab Fab light chain	D [auth L]	220	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.253 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.191	α = 90
b = 192.228	β = 90
c = 65.585	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Ma, X., Starovasnik, M.A.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2014-05-21
  Changes: Source and taxonomy
• Version 1.2: 2014-08-20
  Changes: Source and taxonomy
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary