4K3J

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 110: E2987-E2996

  • DOI: 10.1073/pnas.1302725110

  • 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 ant ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hepatocyte growth factor
A
233Homo sapiensMutation(s): 1 
Gene Names: HGF (HPTA)
Find proteins for P14210 (Homo sapiens)
Go to Gene View: HGF
Go to UniProtKB:  P14210
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hepatocyte growth factor beta chain
B
534Homo sapiensMutation(s): 0 
Gene Names: MET
EC: 2.7.10.1
Find proteins for P08581 (Homo sapiens)
Go to Gene View: MET
Go to UniProtKB:  P08581
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Onartuzumab Fab heavy chain
H
224N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Onartuzumab Fab light chain
L
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.191α = 90.00
b = 192.228β = 90.00
c = 65.585γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASESphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2014-05-21
    Type: Source and taxonomy
  • Version 1.2: 2014-08-20
    Type: Source and taxonomy