+Open data
-Basic information
Entry | Database: PDB / ID: 8tui | ||||||
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Title | Crystal structure of Fab-Lirilumab bound to KIR2DL3 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / KIR2DL3 / complex / lirilumab | ||||||
Function / homology | Function and homology information antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / immune response / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Lorig-Roach, N. / DuBois, R.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2024 Title: Structural basis for the activity and specificity of the immune checkpoint inhibitor lirilumab. Authors: Lorig-Roach, N. / Harpell, N.M. / DuBois, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tui.cif.gz | 252.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tui.ent.gz | 178.4 KB | Display | PDB format |
PDBx/mmJSON format | 8tui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tui_validation.pdf.gz | 836.3 KB | Display | wwPDB validaton report |
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Full document | 8tui_full_validation.pdf.gz | 841.6 KB | Display | |
Data in XML | 8tui_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 8tui_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/8tui ftp://data.pdbj.org/pub/pdb/validation_reports/tu/8tui | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 27793.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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#2: Antibody | Mass: 23548.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
#3: Protein | Mass: 28189.141 Da / Num. of mol.: 1 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIR2DL3, CD158B2, KIRCL23, NKAT2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P43628 |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
Sequence details | Partial proteolysis of the receptor (chain A) may have occurred during crystallization. However, ...Partial proteolysis of the receptor (chain A) may have occurred during crystallization. However, the components of the crystal were not sequenced. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.68 Å3/Da / Density % sol: 26.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 200 mM Potassium Sodium Tartrate and 20%(w/v) PEG 3350 |
-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 PILATUS3 6M / Detector: PIXEL / Date: Jul 27, 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: 2.75→50 Å / Num. obs: 13977 / % possible obs: 98.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 60.85 Å2 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.058 / Rrim(I) all: 0.146 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.75→2.8 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.92 / Num. unique obs: 689 / CC1/2: 0.759 / CC star: 0.929 / Χ2: 0.439 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→46.66 Å / SU ML: 0.4626 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6208 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.5 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→46.66 Å
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Refine LS restraints |
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LS refinement shell |
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