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Yorodumi- PDB-1of2: Crystal structure of HLA-B*2709 complexed with the vasoactive int... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1of2 | ||||||
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Title | Crystal structure of HLA-B*2709 complexed with the vasoactive intestinal peptide type 1 receptor (VIPR) peptide (residues 400-408) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX) / HLA (HUMAN LEUKOCYTE ANTIGEN) | ||||||
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 / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / regulation of membrane depolarization ...: / vasoactive intestinal polypeptide receptor activity / : / G protein-coupled peptide receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / regulation of membrane depolarization / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / 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 / detection of bacterium / 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 / 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 / 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 / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / 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 / antibacterial humoral response / iron ion transport / protein-folding chaperone binding / G alpha (s) signalling events / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response / learning or memory / cell surface receptor signaling pathway / receptor complex / defense response to Gram-positive bacterium / immune response / G protein-coupled receptor signaling pathway / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Hulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2004 Title: Dual, Hla-B27 Subtype-Dependent Conformation of a Self-Peptide Authors: Hulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. #1: Journal: J.Biol.Chem. / Year: 2002 Title: Hla-B27 Subtypes Differentially Associated with Disease Authors: Hulsmeyer, M. / Hillig, R.C. / Volz, A. / Ruhl, M. / Schroder, W. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1of2.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1of2.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 1of2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/1of2 ftp://data.pdbj.org/pub/pdb/validation_reports/of/1of2 | HTTPS FTP |
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-Related structure data
Related structure data | 1ogtC 1k5nS 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: 31951.219 Da / Num. of mol.: 1 / Fragment: EXTRACELLUAR DOMAIN, RESIDUES 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q29846, 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) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01884, UniProt: P61769*PLUS |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1399.694 Da / Num. of mol.: 1 / Fragment: RESIDUES 400-408 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P32241 |
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-Non-polymers , 3 types, 346 molecules
#4: Chemical | #5: Chemical | ChemComp-MN / | #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: 2.9 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: TRIS PH 8.5, 19% PEG 8000 HANGING DROP, TEMPERATURE 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.802 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.802 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.1 Å / Num. obs: 25005 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.12 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.35 / % possible all: 97 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 29.1 Å / % possible obs: 95.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.123 |
Reflection shell | *PLUS % possible obs: 96.8 % / Redundancy: 3 % / Num. unique obs: 2495 / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 4.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K5N Resolution: 2.2→62.02 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.122 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.215 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→62.02 Å
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Refine LS restraints |
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