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Yorodumi- PDB-7fi5: Crystal structure of human MICA mutants in complex with natural k... -
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-Basic information
Entry | Database: PDB / ID: 7fi5 | ||||||
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Title | Crystal structure of human MICA mutants in complex with natural killer cell receptor NKG2D | ||||||
Components |
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Keywords | IMMUNE SYSTEM / NKG2D / MICA / thermal stability | ||||||
Function / homology | Function and homology information immune response to tumor cell / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / gamma-delta T cell activation / natural killer cell mediated cytotoxicity / natural killer cell activation / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / negative regulation of GTPase activity / negative regulation of natural killer cell mediated cytotoxicity ...immune response to tumor cell / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / gamma-delta T cell activation / natural killer cell mediated cytotoxicity / natural killer cell activation / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / negative regulation of GTPase activity / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / T cell costimulation / nitric oxide biosynthetic process / DAP12 interactions / T cell mediated cytotoxicity / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / 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 / response to heat / carbohydrate binding / defense response to virus / killing of cells of another organism / cellular response to lipopolysaccharide / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / defense response to bacterium / immune response / external side of plasma membrane / signaling receptor binding / DNA damage response / cell surface / signal transduction / extracellular space / membrane / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | ||||||
Authors | Cai, W. / Peng, S. / Xu, T. / Tian, Y. / Li, Y. / Liu, J. | ||||||
Citation | Journal: to be published Title: Crystal structure of human MICA mutants in complex with natural killer cell receptor NKG2D Authors: Cai, W. / Peng, S. / Xu, T. / Tian, Y. / Li, Y. / Liu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fi5.cif.gz | 120.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fi5.ent.gz | 91.8 KB | Display | PDB format |
PDBx/mmJSON format | 7fi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/7fi5 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/7fi5 | HTTPS FTP |
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-Related structure data
Related structure data | 7fi6C 7fi7C 7fi8C 7fi9C 1hyrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16110.215 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLRK1, D12S2489E, NKG2D / Production host: Escherichia coli (E. coli) / References: UniProt: P26718 #2: Protein | | Mass: 31817.547 Da / Num. of mol.: 1 / Mutation: Q108H, Q120W, W127F, L146W, Y157F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MICA, PERB11.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q29983 #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.69 Å3/Da / Density % sol: 54.22 % / Mosaicity: 0.22 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 2.2 M Sodium chloride, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.39→19.831 Å / Num. obs: 27866 / % possible obs: 99.1 % / Redundancy: 24.6 % / CC1/2: 1 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.018 / Rrim(I) all: 0.088 / Net I/σ(I): 26.5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1hyr Resolution: 2.39→19.831 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.515 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.315 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 177.92 Å2 / Biso mean: 65.819 Å2 / Biso min: 42.53 Å2
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Refinement step | Cycle: final / Resolution: 2.39→19.831 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.39→2.447 Å / Rfactor Rfree error: 0
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