+Open data
-Basic information
Entry | Database: PDB / ID: 4pr5 | ||||||
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Title | Crystal structure of a HLA-B*35:01-HPVG-D5 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / human leukocyte antigen class I / Epstein-Barr virus / viral escape / T cell receptor / viral immunity / structural biology | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host antigen processing and presentation / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / regulation of DNA replication / TAP binding / protection from natural killer cell mediated cytotoxicity ...symbiont-mediated suppression of host antigen processing and presentation / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / regulation of DNA replication / 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 / 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 / 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 / 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 / defense response / 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 / 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 / positive regulation of immune response / Interferon gamma signaling / 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 / positive regulation of protein binding / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / : / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / endonuclease activity / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / DNA-binding transcription factor activity / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / DNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human herpesvirus 4 (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Yu Chih, L. / Rossjohn, J. / Gras, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: A Molecular Basis for the Interplay between T Cells, Viral Mutants, and Human Leukocyte Antigen Micropolymorphism. Authors: Liu, Y.C. / Chen, Z. / Neller, M.A. / Miles, J.J. / Purcell, A.W. / McCluskey, J. / Burrows, S.R. / Rossjohn, J. / Gras, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pr5.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pr5.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 4pr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/4pr5 ftp://data.pdbj.org/pub/pdb/validation_reports/pr/4pr5 | HTTPS FTP |
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-Related structure data
Related structure data | 4praC 4prbC 4prdC 4preC 4prhC 4priC 4prnC 4prpC 2fyyS 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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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 31940.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30685, 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, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1313.348 Da / Num. of mol.: 1 / Fragment: unp residues 407-417 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: Q3KSS4 |
#4: 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: 2.49 Å3/Da / Density % sol: 50.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.6 Details: 16% PEG 4000, 0.2M ammonium acetate and 0.1M Na-Citrate pH 5.6, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.984 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC-Q210 / Detector: CCD / Date: Jun 12, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. all: 42487 / Num. obs: 42487 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.61 Å2 / Rmerge(I) obs: 0.066 / Χ2: 0.934 / Net I/σ(I): 26.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2FYY Resolution: 1.8→45.286 Å / FOM work R set: 0.8649 / SU ML: 0.48 / σ(F): 1.34 / Phase error: 20.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.329 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.69 Å2 / Biso mean: 20.59 Å2 / Biso min: 1.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→45.286 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %
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