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Yorodumi- PDB-1uqs: The Crystal Structure of Human CD1b with a Bound Bacterial Glycolipid -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uqs | ||||||
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Title | The Crystal Structure of Human CD1b with a Bound Bacterial Glycolipid | ||||||
Components |
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Keywords | GLYCOPROTEIN / LIPID / GMM / CD1B / MHC / ANTIGEN PRESENTATION | ||||||
Function / homology | Function and homology information : / : / regulation of membrane depolarization / 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 / retina homeostasis / positive regulation of ferrous iron binding ...: / : / regulation of membrane depolarization / 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 / retina homeostasis / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / cellular response to lipopolysaccharide / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / endosome membrane / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / intracellular membrane-bounded organelle / innate immune response / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Batuwangala, T. / Shepherd, D. / Gadola, S.D. / Gibson, K.J.C. / Zaccai, N.R. / Besra, G.S. / Cerundolo, V. / Jones, E.Y. | ||||||
Citation | Journal: J Immunol. / Year: 2004 Title: The crystal structure of human CD1b with a bound bacterial glycolipid. Authors: Batuwangala, T. / Shepherd, D. / Gadola, S.D. / Gibson, K.J. / Zaccai, N.R. / Fersht, A.R. / Besra, G.S. / Cerundolo, V. / Jones, E.Y. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uqs.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uqs.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 1uqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uqs_validation.pdf.gz | 752.3 KB | Display | wwPDB validaton report |
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Full document | 1uqs_full_validation.pdf.gz | 787.7 KB | Display | |
Data in XML | 1uqs_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 1uqs_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/1uqs ftp://data.pdbj.org/pub/pdb/validation_reports/uq/1uqs | HTTPS FTP |
-Related structure data
Related structure data | 1gzqS 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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-Components
#1: Protein | Mass: 33088.215 Da / Num. of mol.: 1 / Fragment: FRAGMENT: RESIDUES 18-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET23D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P29016 |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET23D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P01884, UniProt: P61769*PLUS |
#3: Chemical | ChemComp-GMM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 67 % / Description: WEISSENBERG METHOD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 0.1M SODIUM CITRATE PH 5.6, 0.5M AMMONIUM SULFATE, 0.5M LITHIUM SULFATE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-4 / Wavelength: 1.01 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2002 / Details: MIRRORS |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.01 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 11697 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 12.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 34.9 |
Reflection shell | Resolution: 3.1→3.21 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 5.7 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 20 Å / Num. measured all: 150075 / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 5.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GZQ Resolution: 3.1→19.9 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1353771.84 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.6 Å2 / ksol: 0.194067 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.291 / Rfactor Rwork: 0.233 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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