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- PDB-4nqx: Crystal Structure of HLA A*0101 in complex with NP44-S7N, an 9-me... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nqx | ||||||
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Title | Crystal Structure of HLA A*0101 in complex with NP44-S7N, an 9-mer influenza epitope | ||||||
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![]() | Immune System/Viral Protein / immune system / presenting viral epitope / T cell receptor / Immune System-Viral Protein complex | ||||||
Function / homology | ![]() T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / helical viral capsid / 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 ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / helical viral capsid / 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 / T cell receptor binding / detection of bacterium / 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 / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / 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 / viral penetration into host nucleus / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / 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 receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / symbiont entry into host cell / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / host cell nucleus / Neutrophil degranulation / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rossjohn, J. / Gras, S. | ||||||
![]() | ![]() Title: Preexisting CD8+ T-cell immunity to the H7N9 influenza A virus varies across ethnicities. Authors: Quinones-Parra, S. / Grant, E. / Loh, L. / Nguyen, T.H. / Campbell, K.A. / Tong, S.Y. / Miller, A. / Doherty, P.C. / Vijaykrishna, D. / Rossjohn, J. / Gras, S. / Kedzierska, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 945.6 KB | Display | ![]() |
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PDB format | ![]() | 794.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 570.5 KB | Display | ![]() |
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Full document | ![]() | 610.8 KB | Display | |
Data in XML | ![]() | 85.9 KB | Display | |
Data in CIF | ![]() | 122.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nqvSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32703.156 Da / Num. of mol.: 6 / Fragment: UNP residues 25-308 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 6 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1099.235 Da / Num. of mol.: 6 / Fragment: NP44, 9-mer influenza epitope / Mutation: S7N mutation against the epitope in related 4NQV / Source method: obtained synthetically / Source: (synth.) ![]() #4: Water | ChemComp-HOH / | Sequence details | THE 9-MER PEPTIDE NP44 IS INFLUENZA EPITOPE, WITH S7N MUTATION AGAINST THE EPITOPE IN RELATED 4NQV. ...THE 9-MER PEPTIDE NP44 IS INFLUENZA EPITOPE, WITH S7N MUTATION AGAINST THE EPITOPE IN RELATED 4NQV. BUT THE EPITOPE IS SHARED BY MANY STRAINS, THUS IT IS NOT APPROPRIAT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.49 % |
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Crystal grow | Temperature: 277 K / Method: evaporation / pH: 5.6 Details: 0.2M MgCl, 0.1M Na-citrate pH 5.6, 15-20% PEG 6K, EVAPORATION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→119.207 Å / Num. all: 165625 / Num. obs: 165625 / % possible obs: 97.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.65 Å2 / Rsym value: 0.082 / Net I/σ(I): 14 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4NQV Resolution: 2→45.75 Å / Cor.coef. Fo:Fc: 0.9017 / Cor.coef. Fo:Fc free: 0.8928 / Occupancy max: 1 / Occupancy min: 0.24 / SU R Cruickshank DPI: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso max: 150.53 Å2 / Biso mean: 46.8141 Å2 / Biso min: 14.76 Å2
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Refine analyze | Luzzati coordinate error obs: 0.439 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→45.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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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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