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Yorodumi- PDB-6joz: Crystal structure of BRLF peptide from EBV in complex with HLA-A1101. -
+Open data
-Basic information
Entry | Database: PDB / ID: 6joz | ||||||
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Title | Crystal structure of BRLF peptide from EBV in complex with HLA-A1101. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Human Leukocyte Antigen | ||||||
Function / homology | Function and homology information T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / detection of bacterium / T cell receptor binding / 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 / 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 / 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 / positive regulation of type II interferon production / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / 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 / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Huan, X. / Xiao, Z. / Tadwal, V.S. / Ren, E.C. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Crystal structure of suboptimal viral fragments of Epstein Barr Virus Rta peptide-HLA complex that stimulate CD8 T cell response. Authors: Huan, X. / Zhuo, Z. / Xiao, Z. / Ren, E.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6joz.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6joz.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 6joz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/6joz ftp://data.pdbj.org/pub/pdb/validation_reports/jo/6joz | HTTPS FTP |
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-Related structure data
Related structure data | 6jp3C 1x7qS S: Starting model for refinement C: citing same article (ref.) |
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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: 31855.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FRAGMENT: EXTRACELLULAR DOMAIN ALPHA 1, ALPHA 2 AND ALPHA 3. Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pet30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13746, UniProt: P04439*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: pet30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769 | ||
#3: Protein/peptide | Mass: 956.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#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: 2.68 Å3/Da / Density % sol: 54.08 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M LITHIUM SULFATE MONOHYDRATE, 0.1M TRIS-HCL, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→63.08 Å / Num. obs: 101182 / % possible obs: 97 % / Redundancy: 4.4 % / CC1/2: 0.918 / Rrim(I) all: 0.08 / Net I/σ(I): 2.31 |
Reflection shell | Resolution: 1.35→1.385 Å / CC1/2: 0.729 / Rrim(I) all: 0.561 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X7Q Resolution: 1.35→63.08 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.736 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.052 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.427 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→63.08 Å
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