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Yorodumi- PDB-4pp8: Crystal structure of murine NK cell ligand RAE-1 beta in complex ... -
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-Basic information
Entry | Database: PDB / ID: 4pp8 | |||||||||
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Title | Crystal structure of murine NK cell ligand RAE-1 beta in complex with NKG2D | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / MURINE NK CELL LIGAND / RAE-1 BETA / NKG2D / MHC-I PLATFORM | |||||||||
Function / homology | Function and homology information positive regulation of immune response to tumor cell / positive regulation of myeloid dendritic cell activation / susceptibility to natural killer cell mediated cytotoxicity / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / natural killer cell mediated cytotoxicity / natural killer cell activation / positive regulation of macrophage activation / natural killer cell lectin-like receptor binding ...positive regulation of immune response to tumor cell / positive regulation of myeloid dendritic cell activation / susceptibility to natural killer cell mediated cytotoxicity / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / natural killer cell mediated cytotoxicity / natural killer cell activation / positive regulation of macrophage activation / natural killer cell lectin-like receptor binding / positive regulation of natural killer cell activation / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cellular response to exogenous dsRNA / 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 / nitric oxide biosynthetic process / kinase binding / positive regulation of T cell mediated cytotoxicity / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / signaling receptor activity / carbohydrate binding / cellular response to lipopolysaccharide / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / defense response to bacterium / immune response / positive regulation of apoptotic process / external side of plasma membrane / intracellular membrane-bounded organelle / cell surface / extracellular space / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Li, P. / Strong, R.K. | |||||||||
Citation | Journal: Immunity / Year: 2002 Title: Crystal structures of RAE-1beta and its complex with the activating immunoreceptor NKG2D. Authors: Li, P. / McDermott, G. / Strong, R.K. #1: Journal: Immunity / Year: 2000 Title: Retinoic acid early inducible genes define a ligand family for the activating NKG2D receptor in mice. Authors: Cerwenka, A. / Bakker, A.B. / McClanahan, T. / Wagner, J. / Wu, J. / Phillips, J.H. / Lanier, L.L. #2: Journal: Nat.Immunol. / Year: 2000 Title: Ligands for the murine NKG2D receptor: expression by tumor cells and activation of NK cells and macrophages. Authors: Diefenbach, A. / Jamieson, A.M. / Liu, S.D. / Shastri, N. / Raulet, D.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pp8.cif.gz | 228.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pp8.ent.gz | 192.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/4pp8 ftp://data.pdbj.org/pub/pdb/validation_reports/pp/4pp8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 14375.146 Da / Num. of mol.: 2 / Fragment: RAE-1BETA, UNP residues 109-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klrk1, Nkg2d, RAE-1 BETA / Plasmid: PET22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: O54709 #2: Protein | Mass: 20043.744 Da / Num. of mol.: 2 / Fragment: IMMUNORECEPTOR NKG2D, UNP residues 31-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: NKG2D, Raet1b / Plasmid: PET22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: O08603 #3: Chemical | ChemComp-GOL / | #4: 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: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG8000, 0.300M AS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2003 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.77 Å / Num. all: 49287 / Num. obs: 45094 / % possible obs: 91.48 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48.77 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.248 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.167 / ESU R Free: 0.144 / 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: 48.029 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→48.77 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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