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Yorodumi- PDB-2x4r: Crystal structure of MHC CLass I HLA-A2.1 bound to Cytomegaloviru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x4r | ||||||
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Title | Crystal structure of MHC CLass I HLA-A2.1 bound to Cytomegalovirus (CMV) pp65 epitope | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN DOMAIN / HOST-VIRUS INTERACTION / GLYCATION / AMYLOIDOSIS / AMYLOID / PHOTOCLEAVABLE PEPTIDE / IMMUNE RESPONSE | ||||||
Function / homology | Function and homology information viral tegument / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 ...viral tegument / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / endoplasmic reticulum exit site / beta-2-microglobulin binding / 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 / T cell receptor binding / 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 / 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 / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / 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 / antibacterial humoral response / T cell receptor signaling pathway / protein refolding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / 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 / host cell nucleus / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) HUMAN HERPESVIRUS 5 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Celie, P.H.N. / Toebes, M. / Rodenko, B. / Ovaa, H. / Perrakis, A. / Schumacher, T.N.M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Uv-Induced Ligand Exchange in Mhc Class I Protein Crystals. Authors: Celie, P.H.N. / Toebes, M. / Rodenko, B. / Ovaa, H. / Perrakis, A. / Schumacher, T.N.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x4r.cif.gz | 338.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x4r.ent.gz | 279.4 KB | Display | PDB format |
PDBx/mmJSON format | 2x4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/2x4r ftp://data.pdbj.org/pub/pdb/validation_reports/x4/2x4r | HTTPS FTP |
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-Related structure data
Related structure data | 2x4nC 2x4oC 2x4sC 2x4uC 2x70C 1eeyS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XLI BLUE / References: UniProt: P61769 #3: Protein/peptide | Mass: 943.161 Da / Num. of mol.: 2 / Fragment: EPITOPE, RESIDUES 495-503 / Source method: obtained synthetically / Source: (synth.) HUMAN HERPESVIRUS 5 / References: UniProt: P06725 #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | INITIALIZI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 45.5 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 0.1 M MES PH 6.5, 20% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9773 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 6, 2007 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9773 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.373 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 38302 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 3.6 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.59 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EEY Resolution: 2.3→19.978 Å / σ(F): 1.39 / Phase error: 28.85 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.942 Å2 / ksol: 0.345 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.978 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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