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Yorodumi- PDB-1uxs: CRYSTAL STRUCTURE OF HLA-B*2705 COMPLEXED WITH THE LATENT MEMBRAN... -
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-Basic information
Entry | Database: PDB / ID: 1uxs | ||||||
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Title | CRYSTAL STRUCTURE OF HLA-B*2705 COMPLEXED WITH THE LATENT MEMBRANE PROTEIN 2 PEPTIDE (LMP2)OF EPSTEIN-BARR VIRUS | ||||||
Components |
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Keywords | IMMUNE SYSTEM/PEPTIDE / COMPLEX (HLA-PEPTIDE) / IMMUNE SYSTEM / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX) / HLA-B*2705 / EPSTEIN-BARR VIRUS / IMMUNE SYSTEM-PEPTIDE complex | ||||||
Function / homology | Function and homology information : / : / host cell endomembrane system / viral latency / regulation of membrane depolarization / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production ...: / : / host cell endomembrane system / viral latency / regulation of membrane depolarization / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / secretory granule membrane / negative regulation of receptor binding / DAP12 interactions / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / sensory perception of smell / MHC class I protein complex / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of T cell mediated cytotoxicity / positive regulation of cellular senescence / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / antibacterial humoral response / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / cellular response to lipopolysaccharide / symbiont-mediated perturbation of host ubiquitin-like protein modification / defense response to Gram-negative bacterium / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / host cell perinuclear region of cytoplasm / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / signaling receptor binding / focal adhesion / 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) EPSTEIN-BARR VIRUS (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 | 1uxs.cif.gz | 207.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uxs.ent.gz | 166.4 KB | Display | PDB format |
PDBx/mmJSON format | 1uxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uxs_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 1uxs_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | 1uxs_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 1uxs_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/1uxs ftp://data.pdbj.org/pub/pdb/validation_reports/ux/1uxs | HTTPS FTP |
-Related structure data
Related structure data | 1uxwC 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: 31928.160 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.) EPSTEIN-BARR VIRUS (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: 7.5 / Details: 0.1M TRIS, PH 7.5, 15% 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: 1.55→62 Å / Num. obs: 74438 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 4 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K5N Resolution: 1.55→62.02 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.175 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.067 / 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: 17.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→62.02 Å
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