+Open data
-Basic information
Entry | Database: PDB / ID: 1jfm | ||||||
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Title | CRYSTAL STRUCTURE OF MURINE NK CELL LIGAND RAE-1 BETA | ||||||
Components | retinoic acid early transcript beta | ||||||
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 / susceptibility to natural killer cell mediated cytotoxicity / natural killer cell lectin-like receptor binding / positive regulation of natural killer cell activation / positive regulation of macrophage activation / cellular response to exogenous dsRNA / 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 / positive regulation of T cell mediated cytotoxicity / positive regulation of nitric oxide biosynthetic process ...positive regulation of immune response to tumor cell / susceptibility to natural killer cell mediated cytotoxicity / natural killer cell lectin-like receptor binding / positive regulation of natural killer cell activation / positive regulation of macrophage activation / cellular response to exogenous dsRNA / 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 / positive regulation of T cell mediated cytotoxicity / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / cellular response to lipopolysaccharide / defense response to bacterium / immune response / external side of plasma membrane / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.85 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 2 Activating Nkg2D Receptor in Mouse Authors: CERWENKA, A. / BAKKER, A.B. / MCCLANHAN, 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 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 | 1jfm.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jfm.ent.gz | 138 KB | Display | PDB format |
PDBx/mmJSON format | 1jfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jfm_validation.pdf.gz | 396.5 KB | Display | wwPDB validaton report |
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Full document | 1jfm_full_validation.pdf.gz | 452.3 KB | Display | |
Data in XML | 1jfm_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 1jfm_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/1jfm ftp://data.pdbj.org/pub/pdb/validation_reports/jf/1jfm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 20043.744 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: RAE-1beta / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: O08603 #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: 3.9 Å3/Da / Density % sol: 68.5 % / Description: MIR WITH 5 FOLD NCS AVERAGING | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 30% PEG400 + 375mM (NH4)2SO4, pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 / Wavelength: 1.1 Å | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2001 / Details: DOUBLE CRYSTAL | |||||||||
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.85→25 Å / Num. all: 38675 / Num. obs: 37491 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.37 % / Biso Wilson estimate: 88.9 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 37.5 | |||||||||
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 11 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1899 / Rsym value: 0.46 / % possible all: 100 | |||||||||
Reflection | *PLUS Num. obs: 38675 / Redundancy: 10.4 % / Rmerge(I) obs: 0.079 | |||||||||
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: NONE Resolution: 2.85→24.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 283690.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.82 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 89 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→24.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→3.03 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 7.6 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 89 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.403 / % reflection Rfree: 7.8 % / Rfactor Rwork: 0.398 |