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Yorodumi- PDB-3gsq: Crystal structure of the binary complex between HLA-A2 and HCMV N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gsq | ||||||
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Title | Crystal structure of the binary complex between HLA-A2 and HCMV NLV-M5S peptide variant | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / HUMAN CYTOMEGALOVIRUS / PP65 / T CELL RECEPTOR (TCR) / IMMUNE RESPONSE / PUBLIC RESPONSE / IMMUNODOMINANCE / RESTRAINED RESPONSE / HOST-VIRUS INTERACTION / MEMBRANE / MHC I / POLYMORPHISM / IMMUNOGLOBULIN DOMAIN | ||||||
Function / homology | Function and homology information 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 ...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 / early endosome lumen / positive regulation of receptor binding / 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 / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / 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 / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / 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 / endoplasmic reticulum lumen / external side of plasma membrane / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 Å | ||||||
Authors | Reiser, J.-B. / Saulquin, X. / Gras, S. / Debeaupuis, E. / Echasserieau, K. / Kissenpfennig, A. / Legoux, F. / Chouquet, A. / Le Gorrec, M. / Machillot, P. ...Reiser, J.-B. / Saulquin, X. / Gras, S. / Debeaupuis, E. / Echasserieau, K. / Kissenpfennig, A. / Legoux, F. / Chouquet, A. / Le Gorrec, M. / Machillot, P. / Neveu, B. / Thielens, N. / Malissen, B. / Bonneville, M. / Housset, D. | ||||||
Citation | Journal: J.Immunol. / Year: 2009 Title: Structural bases for the affinity-driven selection of a public TCR against a dominant human cytomegalovirus epitope. Authors: Gras, S. / Saulquin, X. / Reiser, J.B. / Debeaupuis, E. / Echasserieau, K. / Kissenpfennig, A. / Legoux, F. / Chouquet, A. / Le Gorrec, M. / Machillot, P. / Neveu, B. / Thielens, N. / ...Authors: Gras, S. / Saulquin, X. / Reiser, J.B. / Debeaupuis, E. / Echasserieau, K. / Kissenpfennig, A. / Legoux, F. / Chouquet, A. / Le Gorrec, M. / Machillot, P. / Neveu, B. / Thielens, N. / Malissen, B. / Bonneville, M. / Housset, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gsq.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gsq.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 3gsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/3gsq ftp://data.pdbj.org/pub/pdb/validation_reports/gs/3gsq | HTTPS FTP |
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-Related structure data
Related structure data | 3gsnC 3gsoC 3gsrC 3gsuC 3gsvC 3gswC 3gsxC 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: 31753.139 Da / Num. of mol.: 1 / Mutation: A245V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA, HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): X90F LaqQ1 / References: UniProt: P01892, UniProt: P04439*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, Beta-2 microglubulin, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): X90F LaqQ1 / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 899.042 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#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: 2.58 Å3/Da / Density % sol: 52.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 9-20% PEG 6000, 0.1M tri-Na Citrate, 0-0.1M NaCl, pH 6.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→50 Å / Num. obs: 27129 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 29.46 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 27.71 |
Reflection shell | Resolution: 2.12→2.19 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 6.7 / Num. measured obs: 4172 / Num. unique all: 1656 / Num. unique obs: 1765 / Rsym value: 0.169 / % possible all: 69.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→14.92 Å / Cor.coef. Fo:Fc: 0.939 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.881 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.63 Å2 / Biso mean: 35.564 Å2 / Biso min: 21.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→14.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.174 Å / Total num. of bins used: 20
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