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Yorodumi- PDB-1uvq: Crystal structure of HLA-DQ0602 in complex with a hypocretin peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uvq | |||||||||
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Title | Crystal structure of HLA-DQ0602 in complex with a hypocretin peptide | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOLOGY / MHC CLASS II / DIABETES / NARCOLEPSY / AUTOIMMUNE DISEASE / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS | |||||||||
Function / homology | Function and homology information immunoglobulin production involved in immunoglobulin-mediated immune response / type 1 orexin receptor binding / type 2 orexin receptor binding / : / Orexin and neuropeptides FF and QRFP bind to their respective receptors / negative regulation of transmission of nerve impulse / positive regulation of transmission of nerve impulse / regulation of neurotransmitter secretion / MHC class II receptor activity / humoral immune response mediated by circulating immunoglobulin ...immunoglobulin production involved in immunoglobulin-mediated immune response / type 1 orexin receptor binding / type 2 orexin receptor binding / : / Orexin and neuropeptides FF and QRFP bind to their respective receptors / negative regulation of transmission of nerve impulse / positive regulation of transmission of nerve impulse / regulation of neurotransmitter secretion / MHC class II receptor activity / humoral immune response mediated by circulating immunoglobulin / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / neuropeptide hormone activity / sleep / protein kinase C-activating G protein-coupled receptor signaling pathway / positive regulation of calcium ion transport / temperature homeostasis / transport vesicle membrane / eating behavior / negative regulation of DNA replication / response to starvation / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / plasma membrane => GO:0005886 / negative regulation of potassium ion transport / humoral immune response / Generation of second messenger molecules / PD-1 signaling / neuropeptide signaling pathway / type II interferon-mediated signaling pathway / rough endoplasmic reticulum / excitatory postsynaptic potential / MHC class II antigen presentation / trans-Golgi network membrane / secretory granule / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / synaptic vesicle / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cold-induced thermogenesis / T cell receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / G alpha (q) signalling events / postsynapse / adaptive immune response / endosome membrane / immune response / lysosomal membrane / Golgi membrane / perinuclear region of cytoplasm / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Siebold, C. / Hansen, B.E. / Wyer, J.R. / Harlos, K. / Esnouf, R.E. / Svejgaard, A. / Bell, J.I. / Strominger, J.L. / Jones, E.Y. / Fugger, L. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Crystal Structure of Hla-Dq0602 that Protects Against Type 1 Diabetes and Confers Strong Susceptibility to Narcolepsy Authors: Siebold, C. / Hansen, B.E. / Wyer, J.R. / Harlos, K. / Esnouf, R.E. / Svejgaard, A. / Bell, J.I. / Strominger, J.L. / Jones, E.Y. / Fugger, L. | |||||||||
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 | 1uvq.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uvq.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 1uvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/1uvq ftp://data.pdbj.org/pub/pdb/validation_reports/uv/1uvq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-HLA CLASS II HISTOCOMPATIBILITY ... , 2 types, 2 molecules AB
#1: Protein | Mass: 22275.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P01907, UniProt: E9PMV2*PLUS |
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#2: Protein | Mass: 23029.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P03992, UniProt: P01920*PLUS |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 3104.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CHAIN C IS COVALENTLY CONNECTED AT THE N-TERMINUS OF CHAIN B VIA A GLYCINE-RICH LINKER. AS PER DEFINITION FOR THE MHC CLASS II MOLECULES, THE CHAINS OF THE PEPTIDE LIGAND (CHAIN C) AND THE ...Details: CHAIN C IS COVALENTLY CONNECTED AT THE N-TERMINUS OF CHAIN B VIA A GLYCINE-RICH LINKER. AS PER DEFINITION FOR THE MHC CLASS II MOLECULES, THE CHAINS OF THE PEPTIDE LIGAND (CHAIN C) AND THE BETA-CHAIN (CHAIN B) SHOULD BE DIFFERENT. Source: (gene. exp.) HOMO SAPIENS (human) / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: O43612 |
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-Sugars , 2 types, 3 molecules
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: Sugar |
-Non-polymers , 4 types, 374 molecules
#5: Chemical | ChemComp-GLY / |
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#7: Chemical | ChemComp-ZN / |
#8: Chemical | ChemComp-ACY / |
#9: 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: 2.71 Å3/Da / Density % sol: 54.27 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 3.8 / Details: pH 3.80 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 3.5 / Method: vapor diffusion, sitting 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: ESRF / Beamline: ID29 / Wavelength: 0.956 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 49489 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.6 / % possible all: 78.7 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 78.7 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.31 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→27.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 25 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.85 Å / Rfactor Rfree: 0.25 |