Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 233.27 kDa 
• Atom Count: 10045 
• Residue Count: 2040 
• Unique protein chains: 4

6AVQ

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

• DOI: 10.2210/pdb6AVQ/pdb
• EMDataResource: EMD-7011

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2017-09-04 Released: 2017-11-01 
• Deposition Author(s): Borst, A.J., James, Z.N., Zagotta, W.N., Ginsberg, M., Rey, F.A., DiMaio, F., Backovic, M., Veesler, D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 35.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 29033288 
• DOI: 10.1016/j.str.2017.09.007
• Primary Citation of Related Structures:  
  6AVU, 6AVR, 6AVQ, 5OPY


• PubMed Abstract: 
  

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.

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Organizational Affiliation: 

Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-V	A	957	Homo sapiens	Mutation(s): 0  Gene Names: ITGAV, MSK8, VNRA, VTNR
Find proteins for P06756 (Homo sapiens) Explore P06756  Go to UniProtKB:  P06756
NIH Common Fund Data Resources
PHAROS  P06756 GTEx  ENSG00000138448

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-3	B	692	Homo sapiens	Mutation(s): 0  Gene Names: ITGB3, GP3A
Find proteins for P05106 (Homo sapiens) Explore P05106  Go to UniProtKB:  P05106
NIH Common Fund Data Resources
PHAROS  P05106 GTEx  ENSG00000259207

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
LM609 Fab heavy chain	H	257	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
LM609 Fab light chain	L	214	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 35.0 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-09-04 
• Released Date: 2017-11-01 
Deposition Author(s): Borst, A.J., James, Z.N., Zagotta, W.N., Ginsberg, M., Rey, F.A., DiMaio, F., Backovic, M., Veesler, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM120553
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008268

Revision History 

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Database references
• Version 1.2: 2018-07-18
  Changes: Data collection
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence