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- PDB-7s8q: Crystal Structure of HLA A*1101 in complex with KTNGNAFIGK, an 10... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7s8q | ||||||
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Title | Crystal Structure of HLA A*1101 in complex with KTNGNAFIGK, an 10-mer epitope from Influenza B | ||||||
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![]() | IMMUNE SYSTEM / HLA A*1101 / influenza B / TCR / T cell | ||||||
Function / homology | ![]() helical viral capsid / 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 / negative regulation of receptor binding / DAP12 interactions / 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 ...helical viral capsid / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / 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 / 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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / sensory perception of smell / 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 / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / symbiont entry into host cell / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / signaling receptor binding / focal adhesion / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nguyen, A.T. / Szeto, C. / Gras, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: HLA-A*11:01-restricted CD8+ T cell immunity against influenza A and influenza B viruses in Indigenous and non-Indigenous people. Authors: Habel, J.R. / Nguyen, A.T. / Rowntree, L.C. / Szeto, C. / Mifsud, N.A. / Clemens, E.B. / Loh, L. / Chen, W. / Rockman, S. / Nelson, J. / Davies, J. / Miller, A. / Tong, S.Y.C. / Rossjohn, J. ...Authors: Habel, J.R. / Nguyen, A.T. / Rowntree, L.C. / Szeto, C. / Mifsud, N.A. / Clemens, E.B. / Loh, L. / Chen, W. / Rockman, S. / Nelson, J. / Davies, J. / Miller, A. / Tong, S.Y.C. / Rossjohn, J. / Gras, S. / Purcell, A.W. / Hensen, L. / Kedzierska, K. / Illing, P.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181 KB | Display | ![]() |
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PDB format | ![]() | 141.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7s8rC ![]() 7s8sC ![]() 4mj5S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32142.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1051.197 Da / Num. of mol.: 2 / Fragment: UNP residues 511-520 / Source method: obtained synthetically / Details: peptide from Influenza B / Source: (synth.) ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG 3350, 0.1M BisTris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→43.5 Å / Num. obs: 53875 / % possible obs: 99.5 % / Redundancy: 13.8 % / Biso Wilson estimate: 32.64 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.08→2.14 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3912 / CC1/2: 0.589 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MJ5 Resolution: 2.08→29.87 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.19 / SU Rfree Blow DPI: 0.162 / SU Rfree Cruickshank DPI: 0.161
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Displacement parameters | Biso max: 116.48 Å2 / Biso mean: 35.06 Å2 / Biso min: 12.9 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.08→29.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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