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- PDB-5fkp: Crystal structure of the mouse CD1d in complex with the p99 peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fkp | |||||||||
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Title | Crystal structure of the mouse CD1d in complex with the p99 peptide | |||||||||
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![]() | IMMUNE SYSTEM / CD1D / ANTIGEN PRESENTATION / ALPHA-HELICAL | |||||||||
Function / homology | ![]() regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-4 production / antigen processing and presentation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of type II interferon production / sensory perception of smell / late endosome / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / lysosome / early endosome / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Girardi, E. / Wang, J. / Zajonc, D.M. | |||||||||
![]() | ![]() Title: Structure of an Alpha-Helical Peptide and Lipopeptide Bound to the Non-Classical Mhc Class I Molecule Cd1D Authors: Girardi, E. / Wang, J. / Zajonc, D.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.1 KB | Display | ![]() |
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PDB format | ![]() | 142.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 990.2 KB | Display | ![]() |
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Full document | ![]() | 994.4 KB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5efiC ![]() 3g08S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32609.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11660.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 2873.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: N-TERMINAL BIOTIN / Source: (synth.) ![]() ![]() |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar |
-Non-polymers , 4 types, 278 molecules ![](data/chem/img/6UL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TAR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TAR.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-6UL / | ||||
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#7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-TAR / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.92 % |
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Crystal grow | Details: 0.2M AMMONIUM TARTRATE AND 20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→55 Å / Num. obs: 47272 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3G08 Resolution: 1.8→49.19 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.39 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→49.19 Å
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