+Open data
-Basic information
Entry | Database: PDB / ID: 4s0u | ||||||
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Title | Crystal structure of NKG2D in complex with ULBP6 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Leukaemia / Graft versus Leukaemia / c-type lectin domain / NKG2D / NKG2DL / affinity and autoimmunity | ||||||
Function / homology | Function and homology information negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / : / Post-translational modification: synthesis of GPI-anchored proteins / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / immune system process / positive regulation of natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway ...negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / : / Post-translational modification: synthesis of GPI-anchored proteins / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / immune system process / positive regulation of natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway / MHC class I protein binding / T cell costimulation / nitric oxide biosynthetic process / viral process / DAP12 interactions / positive regulation of nitric oxide biosynthetic process / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / DAP12 signaling / signaling receptor activity / carbohydrate binding / cellular response to lipopolysaccharide / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / external side of plasma membrane / cell surface / endoplasmic reticulum / signal transduction / extracellular space / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Mohammed, F. / Willcox, B.E. | ||||||
Citation | Journal: Sci Signal / Year: 2017 Title: A disease-linked ULBP6 polymorphism inhibits NKG2D-mediated target cell killing by enhancing the stability of NKG2D ligand binding. Authors: Zuo, J. / Willcox, C.R. / Mohammed, F. / Davey, M. / Hunter, S. / Khan, K. / Antoun, A. / Katakia, P. / Croudace, J. / Inman, C. / Parry, H. / Briggs, D. / Malladi, R. / Willcox, B.E. / Moss, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s0u.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s0u.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 4s0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/4s0u ftp://data.pdbj.org/pub/pdb/validation_reports/s0/4s0u | 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: 14577.496 Da / Num. of mol.: 2 / Fragment: UNP residues 90-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: D12S2489E, KLRK1, NKG2D / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P26718 #2: Protein | | Mass: 20066.877 Da / Num. of mol.: 1 / Fragment: UNP residues 29-203 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAET1L, ULBP6 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q5VY80 #3: 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: 2.35 Å3/Da / Density % sol: 47.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 25% PEG 1500, 0.1M PCB, VAPOR DIFFUSION, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN / Detector: CCD / Date: Sep 15, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→18.7 Å / Num. obs: 18069 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 43.641 Å2 / Rmerge(I) obs: 0.097 / Χ2: 0.932 / Net I/σ(I): 18.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→18.73 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.857 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.2133 / FOM work R set: 0.7675 / SU B: 9.436 / SU ML: 0.23 / SU R Cruickshank DPI: 0.594 / SU Rfree: 0.3129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.594 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 89.72 Å2 / Biso mean: 39.706 Å2 / Biso min: 17.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→18.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.349→2.409 Å / Total num. of bins used: 20
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