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Yorodumi- PDB-3czf: Crystal structure of HLA-B*2709 complexed with the glucagon recep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3czf | ||||||
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Title | Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide (residues 412-420) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX / HLA- B*2709 | ||||||
Function / homology | Function and homology information regulation of glycogen metabolic process / glucagon receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / cellular response to glucagon stimulus / exocytosis / response to starvation / peptide hormone binding ...regulation of glycogen metabolic process / glucagon receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / cellular response to glucagon stimulus / exocytosis / response to starvation / peptide hormone binding / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / cellular response to starvation / hormone-mediated signaling pathway / response to nutrient / guanyl-nucleotide exchange factor activity / 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 / generation of precursor metabolites and energy / 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 / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / 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 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / T cell mediated cytotoxicity / Glucagon signaling in metabolic regulation / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / defense response / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / Glucagon-type ligand receptors / 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 / 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 / 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 / glucose homeostasis / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / protein-folding chaperone binding / T cell differentiation in thymus / protein refolding / G alpha (s) signalling events / G alpha (q) signalling events / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / endosome / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Loll, B. / Fiorillo, M.T. / Rueckert, C. / Saenger, W. / Sorrentino, R. / Ziegler, A. / Uchanska-Ziegler, B. | ||||||
Citation | Journal: Front Immunol / Year: 2020 Title: Conformational Plasticity of HLA-B27 Molecules Correlates Inversely With Efficiency of Negative T Cell Selection. Authors: Loll, B. / Ruckert, C. / Uchanska-Ziegler, B. / Ziegler, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3czf.cif.gz | 212.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3czf.ent.gz | 169.6 KB | Display | PDB format |
PDBx/mmJSON format | 3czf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3czf_validation.pdf.gz | 455.8 KB | Display | wwPDB validaton report |
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Full document | 3czf_full_validation.pdf.gz | 459.9 KB | Display | |
Data in XML | 3czf_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 3czf_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/3czf ftp://data.pdbj.org/pub/pdb/validation_reports/cz/3czf | HTTPS FTP |
-Related structure data
Related structure data | 1k5nS S: Starting model for refinement |
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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: 31951.219 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03989, UniProt: P01889*PLUS | ||
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769 | ||
#3: Protein/peptide | Mass: 1427.708 Da / Num. of mol.: 1 / Fragment: RESIDUES 412-420 / Source method: obtained synthetically Details: THIS SEQUENCE OCCURS NATURALLY IN HOMO SAPIENS (HUMAN) References: UniProt: P47871 | ||
#4: Chemical | #5: 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: 2.85 Å3/Da / Density % sol: 56.89 % |
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Crystal grow | Temperature: 291 K / pH: 7.5 Details: 14% (w/v) PEG 4000, 20mM Tris/HCl pH 7.5, 150mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2003 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→30 Å / Num. obs: 196702 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.043 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.1→1.12 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.288 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K5N Resolution: 1.2→15 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.765 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 10.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.23 Å / Total num. of bins used: 20
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