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Yorodumi- PDB-1uxw: CRYSTAL STRUCTURE OF HLA-B*2709 COMPLEXED WITH THE LATENT MEMBRAN... -
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-Basic information
Entry | Database: PDB / ID: 1uxw | ||||||
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Title | CRYSTAL STRUCTURE OF HLA-B*2709 COMPLEXED WITH THE LATENT MEMBRANE PROTEIN 2 PEPTIDE (LMP2) OF EPSTEIN-BARR VIRUS | ||||||
Components |
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Keywords | IMMUNE SYSTEM/PEPTIDE / IMMUNE SYSTEM-PEPTIDE COMPLEX / COMPLEX (ANTIGEN-PEPTIDE) / IMMUNE SYSTEM / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX) / HLA- B*2709 | ||||||
Function / homology | Function and homology information : / host cell endomembrane system / viral latency / : / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / regulation of membrane depolarization ...: / host cell endomembrane system / viral latency / : / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / regulation of membrane depolarization / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / secretory granule membrane / 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 / lumenal side of endoplasmic reticulum membrane / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / defense response / 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 / 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 / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / early endosome membrane / protein refolding / antibacterial humoral response / symbiont-mediated perturbation of host ubiquitin-like protein modification / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / host cell perinuclear region of cytoplasm / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) HUMAN HERPESVIRUS 4 (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Hulsmeyer, M. / Kozerski, C. / Fiorillo, M.T. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Allele-Dependent Similarity between Viral and Self-Peptide Presentation by Hla-B27 Subtypes Authors: Fiorillo, M.T. / Ruckert, C. / Hulsmeyer, M. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. #1: Journal: J.Exp.Med. / Year: 2004 Title: Dual, Hla-B27 Subtype-Dependent Conformation of a Self-Peptide Authors: Hulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. | ||||||
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 | 1uxw.cif.gz | 111.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uxw.ent.gz | 85.5 KB | Display | PDB format |
PDBx/mmJSON format | 1uxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/1uxw ftp://data.pdbj.org/pub/pdb/validation_reports/ux/1uxw | HTTPS FTP |
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-Related structure data
Related structure data | 1uxsC 1k5nS 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
#1: Protein | Mass: 31951.219 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03989, UniProt: P01889*PLUS | ||
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN DOMAIN, RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01884, UniProt: P61769*PLUS | ||
#3: Protein/peptide | Mass: 1303.586 Da / Num. of mol.: 1 / Fragment: TRANSMEMBRANE DOMAIN, RESIDUES 236-244 / Source method: obtained synthetically / Source: (synth.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus) / References: UniProt: P13285 | ||
#4: Chemical | ChemComp-GOL / #5: 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: 2.9 Å3/Da / Density % sol: 56.9 % |
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Crystal grow | pH: 8.5 / Details: 0.1M TRIS, PH 8.5, 21% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.8856 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→60 Å / Num. obs: 53353 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 4 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K5N Resolution: 1.71→60.86 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.609 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.092 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→60.86 Å
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