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- PDB-4wwk: Crystal structure of human TCR Alpha Chain-TRAV12-3, Beta Chain-T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wwk | ||||||
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Title | Crystal structure of human TCR Alpha Chain-TRAV12-3, Beta Chain-TRBV6-5, Antigen-presenting molecule CD1d, and Beta-2-microglobulin | ||||||
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![]() | IMMUNE SYSTEM / Innate Immunity / NKT | ||||||
Function / homology | ![]() lipid antigen binding / T cell selection / 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 regulation of innate immune response / heterotypic cell-cell adhesion / T cell receptor complex ...lipid antigen binding / T cell selection / 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 regulation of innate immune response / heterotypic cell-cell adhesion / T cell receptor complex / beta-2-microglobulin binding / detection of bacterium / positive regulation of T cell proliferation / cell adhesion molecule binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / recycling endosome membrane / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / histone binding / T cell differentiation in thymus / protein refolding / basolateral plasma membrane / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / lysosome / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Le Nours, J. / Praveena, T. / Pellicci, D.G. / Gherardin, N.A. / Lim, R.T. / Besra, G. / Keshipeddy, A. / Richardson, S.K. / Howell, A.R. / Gras, S. ...Le Nours, J. / Praveena, T. / Pellicci, D.G. / Gherardin, N.A. / Lim, R.T. / Besra, G. / Keshipeddy, A. / Richardson, S.K. / Howell, A.R. / Gras, S. / Godfrey, D.I. / Rossjohn, J. / Uldrich, A.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Atypical natural killer T-cell receptor recognition of CD1d-lipid antigens. Authors: Le Nours, J. / Praveena, T. / Pellicci, D.G. / Gherardin, N.A. / Ross, F.J. / Lim, R.T. / Besra, G.S. / Keshipeddy, S. / Richardson, S.K. / Howell, A.R. / Gras, S. / Godfrey, D.I. / Rossjohn, J. / Uldrich, A.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 320.8 KB | Display | ![]() |
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PDB format | ![]() | 256.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 709.1 KB | Display | ![]() |
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Full document | ![]() | 717 KB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ww1C ![]() 4ww2C ![]() 2po6S 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 , 4 types, 4 molecules ABCD
#1: Protein | Mass: 23231.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 27261.307 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 31495.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein | Mass: 13732.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 1 types, 2 molecules ![](data/chem/img/NAG.gif)
#5: Sugar |
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-Non-polymers , 2 types, 4 molecules ![](data/chem/img/JLS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-JLS / ( |
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#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 18% PEG8000 0.1M CHES 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→65.37 Å / Num. obs: 19363 / % possible obs: 94.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 61.88 Å2 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 3.1→3.27 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.4 / % possible all: 92.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2PO6 Resolution: 3.1→31.61 Å / Cor.coef. Fo:Fc: 0.8953 / Cor.coef. Fo:Fc free: 0.8103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.441
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Displacement parameters | Biso mean: 62.76 Å2
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Refine analyze | Luzzati coordinate error obs: 0.576 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→31.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.27 Å / Total num. of bins used: 10
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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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