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Yorodumi- PDB-3rbg: Crystal structure analysis of Class-I MHC restricted T-cell assoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rbg | ||||||
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Title | Crystal structure analysis of Class-I MHC restricted T-cell associated molecule | ||||||
Components | Cytotoxic and regulatory T-cell molecule | ||||||
Keywords | IMMUNE SYSTEM / IgV / CRTAM / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN | ||||||
Function / homology | Function and homology information detection of tumor cell / regulation of CD8-positive, alpha-beta T cell activation / detection of stimulus / cell recognition / establishment of T cell polarity / lymphocyte migration into lymphoid organs / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / regulation of T cell activation / regulation of T cell differentiation ...detection of tumor cell / regulation of CD8-positive, alpha-beta T cell activation / detection of stimulus / cell recognition / establishment of T cell polarity / lymphocyte migration into lymphoid organs / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / regulation of T cell activation / regulation of T cell differentiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / negative regulation of activated T cell proliferation / immunological synapse / positive regulation of cytokine production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / adaptive immune response / signaling receptor binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Rubinstein, R. / Ramagopal, U.A. / Toro, R. / Nathenson, S.G. / Fiser, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN) | ||||||
Citation | Journal: Structure / Year: 2013 Title: Functional classification of immune regulatory proteins. Authors: Rubinstein, R. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C. / Fiser, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rbg.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rbg.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 3rbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rbg_validation.pdf.gz | 477.1 KB | Display | wwPDB validaton report |
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Full document | 3rbg_full_validation.pdf.gz | 482.4 KB | Display | |
Data in XML | 3rbg_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 3rbg_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/3rbg ftp://data.pdbj.org/pub/pdb/validation_reports/rb/3rbg | HTTPS FTP |
-Related structure data
Related structure data | 1z9mS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | ANALYTICAL ULTRA CENTRIFUGATION STUDIES SUGGESTS IT IS DIMER IN SOLUTION. |
-Components
#1: Protein | Mass: 14246.207 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRTAM / Plasmid: pET-28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: O95727 #2: Chemical | ChemComp-PO4 / #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: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.49 M Sodium Phosphate, 0.91M Potasium Phosphate pH 6.9, Vapor diffusion, Sitting drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.3→40 Å / Num. all: 23676 / Num. obs: 23676 / % possible obs: 98.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.057 / Χ2: 1.369 / Net I/σ(I): 12.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1Z9M Resolution: 2.3→28.47 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2319 / WRfactor Rwork: 0.1997 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.6938 / SU B: 8.227 / SU ML: 0.184 / SU R Cruickshank DPI: 0.0598 / SU Rfree: 0.0449 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.045 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.61 Å2 / Biso mean: 30.1721 Å2 / Biso min: 14.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→28.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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