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Yorodumi- PDB-2h26: human CD1b in complex with endogenous phosphatidylcholine and spacer -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h26 | |||||||||
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Title | human CD1b in complex with endogenous phosphatidylcholine and spacer | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / LIPID / endogenous ligand / phosphatidylcholine / MHC / ANTIGEN PRESENTATION / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information 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 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 ...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 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / endosome membrane / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / 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 / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Garcia-Alles, L.F. / Maveyraud, L. / Vallina, A.T. / Guillet, V. / Mourey, L. | |||||||||
Citation | Journal: Embo J. / Year: 2006 Title: Endogenous phosphatidylcholine and a long spacer ligand stabilize the lipid-binding groove of CD1b. Authors: Garcia-Alles, L.F. / Versluis, K. / Maveyraud, L. / Vallina, A.T. / Sansano, S. / Bello, N.F. / Gober, H.J. / Guillet, V. / de la Salle, H. / Puzo, G. / Mori, L. / Heck, A.J. / De Libero, G. / Mourey, L. | |||||||||
History |
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Remark 600 | HETEROGEN AUTHOR STATES THAT THIS LIGAND IS FROM UNKNOWN ENDOGENOUS LIGAND. TETRACOSYL PALMITATE ...HETEROGEN AUTHOR STATES THAT THIS LIGAND IS FROM UNKNOWN ENDOGENOUS LIGAND. TETRACOSYL PALMITATE WAS MODELLED AS PROPOSITION. THIS STRUCTURE IS PROVIDED JUST AS STARTING HYPOTHESIS. THE REAL IDENTITY OF THIS LIGAND IS A MATTER OF SPECULATION. | |||||||||
Remark 999 | SEQUENCE THE C-TERMINAL RESIDUES ON CD1B ANTIGEN, IDKLGGGLNDIFEAQKIEWHE, IS A BIRA PEPTIDE TAG. ...SEQUENCE THE C-TERMINAL RESIDUES ON CD1B ANTIGEN, IDKLGGGLNDIFEAQKIEWHE, IS A BIRA PEPTIDE TAG. HOWEVER, AMONG THE LAST 20 RESIDUES, ONLY 5 RESIDUES ARE OBSERVED. These 5 RESIDUES ARE MODELLED AS ALA AND NUMBERED 901-905. THE SEQUENCE ALIGNMENT OF THESE FIVE ALA RESIDUES ARE UNKNOWN. THESE RESIDUES ARE CHANGED TO UNK AS UNKNOWN AMINO ACIDS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h26.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h26.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 2h26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/2h26 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/2h26 | HTTPS FTP |
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-Related structure data
Related structure data | 1gzpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the asymmetric unit contains the biological heterodimer |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31623.738 Da / Num. of mol.: 1 / Fragment: extracellular domain of CD1b antigen Mutation: BirA peptide tag (IDKLGGGLNDIFEAQKIEWHE) at C-terminus Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD1B / Plasmid: BCMGSNeo / Production host: Mus musculus (house mouse) / Strain (production host): J558 cell / References: UniProt: P29016 |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Mus musculus (house mouse) / Strain (production host): J558 cell / References: UniProt: P61769 |
-Sugars , 1 types, 2 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 5 types, 270 molecules
#4: Chemical | ChemComp-6PL / ( | ||
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#5: Chemical | ChemComp-6UL / | ||
#6: Chemical | ChemComp-GOL / | ||
#7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 54.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.5 M ammonium sulfate 5 % (v/v) isopropanol 0.1 M Na citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9756 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2005 |
Radiation | Monochromator: Khozu monochromator with dual parallel Si(111) crystals Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→32.72 Å / Num. all: 43311 / Num. obs: 43311 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5545 / Rsym value: 0.198 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GZP Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.867 / SU ML: 0.09 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.135 / ESU R Free: 0.129 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.607 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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