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Yorodumi- PDB-4qrt: Crystal Structure of HLA B*0801 in complex with ELN_YYM, ELNRKMIYM -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qrt | ||||||
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Title | Crystal Structure of HLA B*0801 in complex with ELN_YYM, ELNRKMIYM | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA B*0801 / CMV / TCR / T cell | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host cell cycle progression / 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 / detection of bacterium / positive regulation of ferrous iron binding ...symbiont-mediated perturbation of host cell cycle progression / 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 / 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 / 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 / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / 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 / host cell nucleus / 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 / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human herpesvirus 5 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | ||||||
Authors | Gras, S. / Twist, K.-A. / Rossjohn, J. | ||||||
Citation | Journal: Sci Rep / Year: 2014 Title: Molecular imprint of exposure to naturally occurring genetic variants of human cytomegalovirus on the T cell repertoire. Authors: Smith, C. / Gras, S. / Brennan, R.M. / Bird, N.L. / Valkenburg, S.A. / Twist, K.A. / Burrows, J.M. / Miles, J.J. / Chambers, D. / Bell, S. / Campbell, S. / Kedzierska, K. / Burrows, S.R. / ...Authors: Smith, C. / Gras, S. / Brennan, R.M. / Bird, N.L. / Valkenburg, S.A. / Twist, K.A. / Burrows, J.M. / Miles, J.J. / Chambers, D. / Bell, S. / Campbell, S. / Kedzierska, K. / Burrows, S.R. / Rossjohn, J. / Khanna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qrt.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qrt.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qrt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qrt_validation.pdf.gz | 451.2 KB | Display | wwPDB validaton report |
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Full document | 4qrt_full_validation.pdf.gz | 456.9 KB | Display | |
Data in XML | 4qrt_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 4qrt_validation.cif.gz | 37.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/4qrt ftp://data.pdbj.org/pub/pdb/validation_reports/qr/4qrt | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 31927.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30460, UniProt: P01889*PLUS |
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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) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1199.486 Da / Num. of mol.: 1 / Fragment: unp residues 51-59 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 5 / References: UniProt: Q9YRL8 |
#4: Chemical | ChemComp-EDO / |
#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: 2.56 Å3/Da / Density % sol: 51.92 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M ammonium acetate, 16% PEG 4K, 0.1 tri-Na citrate, pH 5.6, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 31, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→111.5 Å / Num. all: 111044 / Num. obs: 111044 / % possible obs: 97.6 % / Redundancy: 4.6 % / Rsym value: 0.082 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→19.822 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 19.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.894 Å2 / ksol: 0.339 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.22 Å2 / Biso mean: 18.9744 Å2 / Biso min: 5.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→19.822 Å
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