+Open data
-Basic information
Entry | Database: PDB / ID: 6u6v | ||||||
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Title | Crystal structure of human PD-1H / VISTA | ||||||
Components | V-type immunoglobulin domain-containing suppressor of T-cell activation | ||||||
Keywords | IMMUNE SYSTEM / T cell co-inhibition / immunoglobulin-like | ||||||
Function / homology | Function and homology information positive regulation of collagen catabolic process / negative regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of endopeptidase activity / negative regulation of alpha-beta T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-17 production / zymogen activation / negative regulation of interleukin-10 production / negative regulation of type II interferon production ...positive regulation of collagen catabolic process / negative regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of endopeptidase activity / negative regulation of alpha-beta T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-17 production / zymogen activation / negative regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / endopeptidase activator activity / regulation of immune response / positive regulation of cell migration / positive regulation of gene expression / enzyme binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Slater, B.T. / Han, X. / Chen, L. / Xiong, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structural insight into T cell coinhibition by PD-1H (VISTA). Authors: Slater, B.T. / Han, X. / Chen, L. / Xiong, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u6v.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u6v.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 6u6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/6u6v ftp://data.pdbj.org/pub/pdb/validation_reports/u6/6u6v | HTTPS FTP |
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-Related structure data
Similar structure data |
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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: Protein | Mass: 19678.971 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VSIR, C10orf54, SISP1, VISTA, PP2135, UNQ730/PRO1412 / Plasmid: pcDNA3.4 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q9H7M9 |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 28.18 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 6 Details: 0.3 ul protein in HBS with 0.3 ul of crystallization buffer consisting of 100 mM Bis-Tris:HCl pH 6.0 and 28% (v/v) polyethylene glycol monomethyl ether (MW 2000) (Sigma-Aldrich) under a drop ...Details: 0.3 ul protein in HBS with 0.3 ul of crystallization buffer consisting of 100 mM Bis-Tris:HCl pH 6.0 and 28% (v/v) polyethylene glycol monomethyl ether (MW 2000) (Sigma-Aldrich) under a drop of paraffin oil and silicon oil in a 2:1 ratio |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 10041 / % possible obs: 95.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.061 / Rrim(I) all: 0.115 / Χ2: 0.946 / Net I/σ(I): 7.4 / Num. measured all: 34332 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→41.89 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 13.498 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.175 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 106.51 Å2 / Biso mean: 38.877 Å2 / Biso min: 23.04 Å2
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Refinement step | Cycle: final / Resolution: 1.9→41.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -3.9577 Å / Origin y: -8.0349 Å / Origin z: 54.6787 Å
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