4K3J

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


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 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Department of Translational Oncology, Genentech, Inc., South San Francisco, CA 94080, USA. merchant.mark@gene.com


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor233Homo sapiensMutation(s): 1 
Gene Names: HGFHPTA
UniProt & NIH Common Fund Data Resources
Find proteins for P14210 (Homo sapiens)
Explore P14210 
Go to UniProtKB:  P14210
PHAROS:  P14210
GTEx:  ENSG00000019991 
Entity Groups  
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UniProt GroupP14210
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor beta chain534Homo sapiensMutation(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
GTEx:  ENSG00000105976 
Entity Groups  
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UniProt GroupP08581
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Onartuzumab Fab heavy chainC [auth H]224Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Onartuzumab Fab light chainD [auth L]220Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
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 = 128.191α = 90
b = 192.228β = 90
c = 65.585γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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