+Open data
-Basic information
Entry | Database: PDB / ID: 5opy | ||||||||||||
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Title | Crystal structure of anti-alphaVbeta3 integrin Fab LM609 | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM / Antigen-binding fragment / Fab / LM609 | ||||||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||||||||
Authors | Backovic, M. / Veesler, D. / Borst, A.J. / James, Z.M. / Zagotta, W. / Ginsberg, M. / Rey, F.A. / DiMaio, F. | ||||||||||||
Funding support | France, United States, 3items
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Citation | Journal: Structure / Year: 2017 Title: The Therapeutic Antibody LM609 Selectively Inhibits Ligand Binding to Human αβ Integrin via Steric Hindrance. Authors: Andrew J Borst / Zachary M James / William N Zagotta / Mark Ginsberg / Felix A Rey / Frank DiMaio / Marija Backovic / David Veesler / Abstract: The LM609 antibody specifically recognizes αβ integrin and inhibits angiogenesis, bone resorption, and viral infections in an arginine-glycine-aspartate-independent manner. LM609 entered phase II ...The LM609 antibody specifically recognizes αβ 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 αβ-targeted radioimmunotherapy. To elucidate the mechanisms of recognition and inhibition of αβ integrin, we solved the structure of the LM609 antigen-binding fragment by X-ray crystallography and determined its binding affinity for αβ. Using single-particle electron microscopy, we show that LM609 binds at the interface between the β-propeller domain of the α chain and the βI domain of the β 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. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5opy.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5opy.ent.gz | 74 KB | Display | PDB format |
PDBx/mmJSON format | 5opy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5opy_validation.pdf.gz | 431.7 KB | Display | wwPDB validaton report |
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Full document | 5opy_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 5opy_validation.xml.gz | 18 KB | Display | |
Data in CIF | 5opy_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/5opy ftp://data.pdbj.org/pub/pdb/validation_reports/op/5opy | HTTPS FTP |
-Related structure data
Related structure data | 7011C 7012C 7013C 6avqC 6avrC 6avuC 2adgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 27223.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell: Hybrydoma / Cell line (production host): Schneider S2 / Production host: Drosophila melanogaster (fruit fly) |
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#2: Antibody | Mass: 23628.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell: Hybrydoma / Cell line (production host): Schneider S2 / Production host: Drosophila melanogaster (fruit fly) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.48 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 30% PEG 4,000 and 0.2M CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→45.16 Å / Num. obs: 19133 / % possible obs: 99.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 39.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.26→2.36 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 9085 / CC1/2: 0.759 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ADG Resolution: 2.26→45.16 Å / Cor.coef. Fo:Fc: 0.9313 / Cor.coef. Fo:Fc free: 0.8944 / SU R Cruickshank DPI: 0.383 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.425 / SU Rfree Blow DPI: 0.247 / SU Rfree Cruickshank DPI: 0.244
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Displacement parameters | Biso mean: 35.44 Å2
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Refine analyze | Luzzati coordinate error obs: 0.324 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.26→45.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.38 Å / Total num. of bins used: 10
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