[English] 日本語
Yorodumi- PDB-2a83: Crystal structure of hla-b*2705 complexed with the glucagon recep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a83 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of hla-b*2705 complexed with the glucagon receptor (gr) peptide (residues 412-420) | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX) / HLA-B*2705 | ||||||
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 / response to starvation / cellular response to glucagon stimulus / exocytosis / 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 / response to starvation / cellular response to glucagon stimulus / exocytosis / peptide hormone binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 starvation / detection of bacterium / hormone-mediated signaling pathway / guanyl-nucleotide exchange factor activity / response to nutrient / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / generation of precursor metabolites and energy / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / Glucagon signaling in metabolic regulation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / regulation of erythrocyte differentiation / 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 / Glucagon-type ligand receptors / positive regulation of T cell cytokine production / MHC class I protein complex / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / glucose homeostasis / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / G alpha (s) signalling events / protein refolding / early endosome membrane / G alpha (q) signalling events / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / cell surface receptor signaling pathway / endosome / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Ruckert, C. / Fiorillo, M.T. / Loll, B. / Moretti, R. / Biesiadka, J. / Saenger, W. / Ziegler, A. / Sorrentino, R. / Uchanska-Ziegler, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Conformational dimorphism of self-peptides and molecular mimicry in a disease-associated HLA-B27 subtype. Authors: Ruckert, C. / Fiorillo, M.T. / Loll, B. / Moretti, R. / Biesiadka, J. / Saenger, W. / Ziegler, A. / Sorrentino, R. / Uchanska-Ziegler, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2a83.cif.gz | 205.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2a83.ent.gz | 162 KB | Display | PDB format |
PDBx/mmJSON format | 2a83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/2a83 ftp://data.pdbj.org/pub/pdb/validation_reports/a8/2a83 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1jgeS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31928.160 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) / Gene: HLA-B, HLAB / Plasmid: pHN1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q29846, UniProt: P01889*PLUS |
---|---|
#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) / Gene: B2M / Plasmid: pHN1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61769 |
-Protein/peptide , 1 types, 1 molecules C
#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*PLUS |
---|
-Non-polymers , 3 types, 683 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 14% PEG4000,100mM Tris/HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
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: 1.4→50 Å / Num. all: 97993 / Num. obs: 97993 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.039 / Χ2: 1.182 |
Reflection shell | Resolution: 1.4→1.42 Å / % possible obs: 87.7 % / Rmerge(I) obs: 0.112 / Num. measured obs: 4386 / Χ2: 1.12 / % possible all: 87.7 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JGE Resolution: 1.4→28.99 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.953 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→28.99 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
|