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Yorodumi- PDB-8rng: Crystal structure of HLA B*18:01 in complex with TEVETYVL, an 8-m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rng | ||||||
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Title | Crystal structure of HLA B*18:01 in complex with TEVETYVL, an 8-mer epitope from Influenza A | ||||||
Components |
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Keywords | IMMUNE SYSTEM / human leukocyte antigen / major histocompatibility complex / HLA-B*18:01 / Influenza A | ||||||
Function / homology | Function and homology information antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / viral budding from plasma membrane / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 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 / viral budding from plasma membrane / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 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 / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / 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 / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / structural constituent of virion / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Murdolo, L.D. / Maddumage, J.C. / Gras, S. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: Crystal structure of HLA B*18:01 in complex with TEVETYVL, an 8-mer epitope from Influenza A Authors: Murdolo, L.D. / Maddumage, J.C. / Gras, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rng.cif.gz | 125.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rng.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 8rng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/8rng ftp://data.pdbj.org/pub/pdb/validation_reports/rn/8rng | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31747.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A167RQK8 |
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#3: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769 |
-Protein/peptide , 1 types, 1 molecules C
#2: Protein/peptide | Mass: 953.044 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Influenza A virus (A/Memphis/18/1978(H3N2)) References: UniProt: Q2PIM0 |
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-Non-polymers , 3 types, 308 molecules
#4: Chemical | ChemComp-EDO / | ||
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#5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.54 Å3/Da / Density % sol: 51.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Potassium Nitrate, 20% w/v PEG 3350 at pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953732 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→46.02 Å / Num. obs: 81219 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 10.92 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.45→1.47 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3941 / CC1/2: 0.707 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→46.02 Å / SU ML: 0.1577 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.1338 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→46.02 Å
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Refine LS restraints |
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LS refinement shell |
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