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Yorodumi- PDB-1xr8: Crystal Structures of HLA-B*1501 in Complex with Peptides from Hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xr8 | ||||||
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Title | Crystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and Epstein-Barr Virus EBNA-3 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / major histocompatibility antigen / MHC / HLA / HLA-B62 / HLA-B*1501 / complex (antigen-peptide) | ||||||
Function / homology | Function and homology information host cell nuclear matrix / DNA-templated viral transcription / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib ...host cell nuclear matrix / DNA-templated viral transcription / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / 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 / defense response / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / 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: 2.3 Å | ||||||
Authors | Roder, G. / Blicher, T. / Johannessen, B.R. / Kristensen, O. / Buus, S. / Gajhede, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype Authors: Roder, G. / Blicher, T. / Justesen, S. / Johannesen, B. / Kristensen, O. / Kastrup, J. / Buus, S. / Gajhede, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xr8.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xr8.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 1xr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/1xr8 ftp://data.pdbj.org/pub/pdb/validation_reports/xr/1xr8 | HTTPS FTP |
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-Related structure data
Related structure data | 1xr9C 1a1mS C: citing same article (ref.) 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31958.195 Da / Num. of mol.: 1 / Fragment: residues (1-276) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-Bw62.1 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30464, UniProt: P01889*PLUS |
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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 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1026.146 Da / Num. of mol.: 1 / Fragment: residues (274-282) / Source method: obtained synthetically / Details: chemical synthesis / References: UniProt: P12977 |
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-Non-polymers , 4 types, 229 molecules
#4: Chemical | ChemComp-PG4 / | ||
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#5: Chemical | ChemComp-URE / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M MgAc4H20, 0.1M Na-cacodylate, pH 6.5, 20% w/v PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.969 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 28, 2004 |
Radiation | Monochromator: Bent diamond crystal, horizontally focusing (R = 12 m) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.969 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.44 Å / Num. all: 20977 / Num. obs: 19549 / % possible obs: 93.19 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 29.855 Å2 / Rsym value: 0.104 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.9 / Num. measured all: 10859 / Num. unique all: 2868 / Rsym value: 0.339 / % possible all: 96.29 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A1M Resolution: 2.3→19.437 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.093 / SU ML: 0.152 / SU R Cruickshank DPI: 0.34 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUHGOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.975 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.437 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.35 Å / Total num. of bins used: 20
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