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Yorodumi- PDB-5ib4: Crystal structure of HLA-B*27:05 complexed with the self-peptide ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ib4 | ||||||
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Title | Crystal structure of HLA-B*27:05 complexed with the self-peptide pVIPR and Nickel | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNE SYSTEM-COMPLEX / MHC MAJOR HISTOCOMPATIBILITY COMPLEX) / HLA- B*2705 | ||||||
Function / homology | Function and homology information vasoactive intestinal polypeptide receptor activity / G protein-coupled peptide receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / TAP binding / protection from natural killer cell mediated cytotoxicity ...vasoactive intestinal polypeptide receptor activity / G protein-coupled peptide receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / secretory granule membrane / 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 / 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 / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / 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 / defense response / MHC class I protein complex / Glucagon-type ligand receptors / 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 / 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 / Interferon alpha/beta signaling / 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 / protein-folding chaperone binding / early endosome membrane / protein refolding / G alpha (s) signalling events / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / receptor complex / immune response / G protein-coupled receptor signaling pathway / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / positive regulation of cell population proliferation / 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 / Resolution: 1.95 Å | ||||||
Authors | Janke, R. / Ballaschk, M. / Schmieder, P. / Uchanska-Ziegler, B. / Ziegler, A. / Loll, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Metal-triggered conformational reorientation of a self-peptide bound to a disease-associated HLA-B*27 subtype. Authors: Driller, R. / Ballaschk, M. / Schmieder, P. / Uchanska-Ziegler, B. / Ziegler, A. / Loll, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ib4.cif.gz | 185.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ib4.ent.gz | 147 KB | Display | PDB format |
PDBx/mmJSON format | 5ib4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/5ib4 ftp://data.pdbj.org/pub/pdb/validation_reports/ib/5ib4 | HTTPS FTP |
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-Related structure data
Related structure data | 5ib1C 5ib2C 5ib3C 5ib5C 1of2S 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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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31928.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03989, UniProt: P01889*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, CDABP0092, HDCMA22P / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1399.694 Da / Num. of mol.: 1 / Fragment: UNP residues 400-408 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P32241 |
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-Non-polymers , 3 types, 199 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.87 Å3/Da / Density % sol: 57.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris HCl, 16% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.127 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 10, 2012 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→35 Å / Num. obs: 69349 / % possible obs: 94.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.995 / Net I/σ(I): 14.76 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 6.43 / % possible all: 65.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OF2 Resolution: 1.95→34.122 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.45 / Phase error: 19.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→34.122 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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