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Yorodumi- PDB-8fwh: Crystal structure of bivalent antibody Fab fragment of Anti-human... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fwh | ||||||
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Title | Crystal structure of bivalent antibody Fab fragment of Anti-human LAG3 (22D2) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / inhibitory receptors | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.833 Å | ||||||
Authors | Mishra, A.K. / Agnihotri, P. / Mariuzza, R.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2023 Title: CryoEM structure of a therapeutic antibody (favezelimab) bound to human LAG3 determined using a bivalent Fab as fiducial marker. Authors: Arjun K Mishra / Salman Shahid / Sharanbasappa S Karade / Pragati Agnihotri / Alexander Kolesnikov / S Saif Hasan / Roy A Mariuzza / Abstract: Lymphocyte activation gene 3 protein (LAG3) is an inhibitory receptor that is upregulated on exhausted T cells in tumors. LAG3 is a major target for cancer immunotherapy with many anti-LAG3 ...Lymphocyte activation gene 3 protein (LAG3) is an inhibitory receptor that is upregulated on exhausted T cells in tumors. LAG3 is a major target for cancer immunotherapy with many anti-LAG3 antibodies in clinical trials. However, there is no structural information on the epitopes recognized by these antibodies. We determined the single-particle cryoEM structure of a therapeutic antibody (favezelimab) bound to LAG3 to 3.5 Å resolution, revealing that favezelimab targets the LAG3-binding site for MHC class II, its canonical ligand. The small size of the complex between the conventional (monovalent) Fab of favezelimab and LAG3 (∼100 kDa) presented a challenge for cryoEM. Accordingly, we engineered a bivalent version of Fab favezelimab that doubled the size of the Fab-LAG3 complex and conferred a highly identifiable shape to the complex that facilitated particle selection and orientation for image processing. This study establishes bivalent Fabs as new fiducial markers for cryoEM analysis of small proteins. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fwh.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fwh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8fwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fwh_validation.pdf.gz | 678.1 KB | Display | wwPDB validaton report |
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Full document | 8fwh_full_validation.pdf.gz | 685 KB | Display | |
Data in XML | 8fwh_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 8fwh_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/8fwh ftp://data.pdbj.org/pub/pdb/validation_reports/fw/8fwh | HTTPS FTP |
-Related 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: 23959.947 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK 293 expi / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23688.984 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK 293 expi / Production host: Homo sapiens (human) |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.26 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Tris-HCl, pH 7.5, 0.2 M sodium chloride, 10% w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→85.57 Å / Num. obs: 13587 / % possible obs: 92.9 % / Redundancy: 2 % / CC1/2: 0.98 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.83→2.9 Å / Num. unique obs: 13515 / CC1/2: 0.68 / CC star: 0.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6WKM Resolution: 2.833→42.75 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 20.341 / SU ML: 0.365 / Cross valid method: FREE R-VALUE / ESU R: 2.956 / ESU R Free: 0.407 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.833→42.75 Å
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Refine LS restraints |
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LS refinement shell |
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