6AVQ

The Therapeutic Antibody LM609 Selectively Inhibits Ligand Binding to Human alpha-V beta-3 Integrin via Steric Hindrance


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Therapeutic Antibody LM609 Selectively Inhibits Ligand Binding to Human alpha V beta 3 Integrin via Steric Hindrance.

Borst, A.J.James, Z.M.Zagotta, W.N.Ginsberg, M.Rey, F.A.DiMaio, F.Backovic, M.Veesler, D.

(2017) Structure 25: 1732-1739.e5

  • DOI: 10.1016/j.str.2017.09.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The LM609 antibody specifically recognizes α <sub>V </sub>β <sub>3 </sub> integrin and inhibits angiogenesis, bone resorption, and viral infections in an arginine-glycine-aspartate-independent manner. LM609 entered phase II clinical trials for the tr ...

    The LM609 antibody specifically recognizes α V β 3 integrin and inhibits angiogenesis, bone resorption, and viral infections in an arginine-glycine-aspartate-independent manner. LM609 entered phase II clinical trials for the treatment of several cancers and was also used for α V β 3 -targeted radioimmunotherapy. To elucidate the mechanisms of recognition and inhibition of α V β 3 integrin, we solved the structure of the LM609 antigen-binding fragment by X-ray crystallography and determined its binding affinity for α V β 3 . Using single-particle electron microscopy, we show that LM609 binds at the interface between the β-propeller domain of the α V chain and the βI domain of the β 3 chain, near the RGD-binding site, of all observed integrin conformational states. Integrating these data with fluorescence size-exclusion chromatography, we demonstrate that LM609 sterically hinders access of large ligands to the RGD-binding pocket, without obstructing it. This work provides a structural framework to expedite future efforts utilizing LM609 as a diagnostic or therapeutic tool.


    Organizational Affiliation

    Unité de Virologie Structurale, Institut Pasteur, Paris, France; CNRS UMR 3569 Virologie, Paris, France. Electronic address: marija@pasteur.fr.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Department of Hematology and Oncology, University of California at San Diego, La Jolla, CA 92093-0726, USA.,Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA.,Unité de Virologie Structurale, Institut Pasteur, Paris, France; CNRS UMR 3569 Virologie, Paris, France.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Electronic address: dveesler@uw.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-V
A
957Homo sapiensMutation(s): 0 
Gene Names: ITGAV (MSK8, VNRA, VTNR)
Find proteins for P06756 (Homo sapiens)
Go to Gene View: ITGAV
Go to UniProtKB:  P06756
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin beta-3
B
692Homo sapiensMutation(s): 0 
Gene Names: ITGB3 (GP3A)
Find proteins for P05106 (Homo sapiens)
Go to Gene View: ITGB3
Go to UniProtKB:  P05106
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LM609 Fab heavy chain
H
257N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
LM609 Fab light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States1R01GM120553
National Institutes of Health/National Institute of General Medical SciencesUnited States Minor Outlying IslandsT32GM008268

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Data collection