+Open data
-Basic information
Entry | Database: PDB / ID: 3bp5 | ||||||
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Title | Crystal structure of the mouse PD-1 and PD-L2 complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / PD-1 / PD-L2 / Complex / Costimulation / Glycoprotein / Immunoglobulin domain / Membrane / Transmembrane / Receptor | ||||||
Function / homology | Function and homology information negative regulation of tolerance induction / regulatory T cell apoptotic process / PD-1 signaling / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production ...negative regulation of tolerance induction / regulatory T cell apoptotic process / PD-1 signaling / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / regulation of immune response / negative regulation of T cell proliferation / positive regulation of T cell proliferation / T cell costimulation / cellular response to lipopolysaccharide / adaptive immune response / cell surface receptor signaling pathway / immune response / external side of plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yan, Q. / Lazar-Molnar, E. / Cao, E. / Ramagopal, U.A. / Toro, R. / Nathenson, S.G. / Almo, S.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Crystal structure of the complex between programmed death-1 (PD-1) and its ligand PD-L2. Authors: Lazar-Molnar, E. / Yan, Q. / Cao, E. / Ramagopal, U. / Nathenson, S.G. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bp5.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bp5.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/3bp5 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/3bp5 | HTTPS FTP |
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-Related structure data
Related structure data | 3bovC 1npuS 1pkqS 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: Protein | Mass: 13176.714 Da / Num. of mol.: 1 / Fragment: Extrocellular domain / Mutation: C50S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdcd1, Pd1 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q02242 |
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#2: Protein | Mass: 22797.139 Da / Num. of mol.: 1 / Fragment: Extrocellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdcd1lg2, B7dc, Btdc, Cd273, Pdl2 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q9WUL5 |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.55 Å3/Da / Density % sol: 51.68 % |
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Crystal grow | Temperature: 291 K / Method: sitting drop / pH: 8.5 Details: 20% PEG 6000, 0.1 M Tris pH 8.5, Sitting drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→30 Å / Num. obs: 39403 / % possible obs: 99.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1npu, 1pkq Resolution: 1.8→24.95 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.743 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.223 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→24.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.843 Å / Total num. of bins used: 20
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