+Open data
-Basic information
Entry | Database: PDB / ID: 6wkm | ||||||
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Title | Fab Fragment of Anti-human LAG3 antibody (22D2) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Anti Human LAG3 | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Agnihotri, P. / Mishra, A.K. / 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 | 6wkm.cif.gz | 124.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wkm.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 6wkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/6wkm ftp://data.pdbj.org/pub/pdb/validation_reports/wk/6wkm | HTTPS FTP |
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-Related structure data
Related structure data | 8fwhC 8so3C 8sr0C 1mimS 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: 25288.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23688.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
#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: 2.58 Å3/Da / Density % sol: 52.31 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, sodium phosphate dibasic, sodium chloride PH range: 8-8.5 |
-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: 0.9796 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2019 |
Radiation | Monochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.65 Å / Num. obs: 29501 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.04 / Rrim(I) all: 0.08 / Χ2: 1.23 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2378 / CC1/2: 0.95 / Rpim(I) all: 0.18 / Rrim(I) all: 0.34 / Χ2: 0.62 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1mim Resolution: 2.1→45.61 Å / SU ML: 0.2451 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.3459 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→45.61 Å
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Refine LS restraints |
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LS refinement shell |
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