+Open data
-Basic information
Entry | Database: PDB / ID: 6ng9 | ||||||
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Title | Crystal structure of human CD160 | ||||||
Components | CD160 antigen | ||||||
Keywords | IMMUNE SYSTEM / CD160 / HVEM / BTLA / gD | ||||||
Function / homology | Function and homology information positive regulation of natural killer cell mediated immune response to tumor cell / activating MHC class I receptor activity / negative regulation of CD4-positive, alpha-beta T cell costimulation / negative regulation of adaptive immune memory response / MHC class I protein complex binding / mucosal immune response / MHC class Ib receptor activity / positive regulation of natural killer cell degranulation / MHC class I receptor activity / positive regulation of endothelial cell apoptotic process ...positive regulation of natural killer cell mediated immune response to tumor cell / activating MHC class I receptor activity / negative regulation of CD4-positive, alpha-beta T cell costimulation / negative regulation of adaptive immune memory response / MHC class I protein complex binding / mucosal immune response / MHC class Ib receptor activity / positive regulation of natural killer cell degranulation / MHC class I receptor activity / positive regulation of endothelial cell apoptotic process / positive regulation of natural killer cell cytokine production / negative regulation of T cell receptor signaling pathway / positive regulation of natural killer cell mediated cytotoxicity / side of membrane / T cell costimulation / negative regulation of angiogenesis / phosphatidylinositol 3-kinase/protein kinase B signal transduction / kinase binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / angiogenesis / defense response to Gram-negative bacterium / adaptive immune response / signaling receptor binding / innate immune response / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.954 Å | ||||||
Authors | Liu, W. / Bonanno, J. / Almo, S.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2019 Title: Structural Basis of CD160:HVEM Recognition. Authors: Liu, W. / Garrett, S.C. / Fedorov, E.V. / Ramagopal, U.A. / Garforth, S.J. / Bonanno, J.B. / 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 | 6ng9.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ng9.ent.gz | 41.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ng9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/6ng9 ftp://data.pdbj.org/pub/pdb/validation_reports/ng/6ng9 | HTTPS FTP |
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-Related structure data
Related structure data | 6ng3C 6nggSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13178.024 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD160, BY55 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpB1GAP_S (others) References: UniProt: O95971 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium Formate, 0.1 M Tris, pH8.5 and 30% (W/V) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9786 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 16516 / % possible obs: 99.8 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.95→1.99 Å / Rmerge(I) obs: 0.935 / Num. unique obs: 1546 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NGG Resolution: 1.954→35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.463 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.171 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.408 Å2
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Refinement step | Cycle: 1 / Resolution: 1.954→35 Å
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Refine LS restraints |
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