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- PDB-1s9v: Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 1s9v | ||||||
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Title | Crystal structure of HLA-DQ2 complexed with deamidated gliadin peptide | ||||||
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![]() | IMMUNE SYSTEM / HLA-DQ2 | ||||||
Function / homology | ![]() immunoglobulin production involved in immunoglobulin-mediated immune response / : / MHC class II receptor activity / humoral immune response mediated by circulating immunoglobulin / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / humoral immune response / Generation of second messenger molecules / PD-1 signaling ...immunoglobulin production involved in immunoglobulin-mediated immune response / : / MHC class II receptor activity / humoral immune response mediated by circulating immunoglobulin / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / humoral immune response / Generation of second messenger molecules / PD-1 signaling / type II interferon-mediated signaling pathway / MHC class II antigen presentation / trans-Golgi network membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / adaptive immune response / endosome membrane / immune response / lysosomal membrane / Golgi membrane / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, C.-Y. / Quarsten, H. / Bergseng, E. / Khosla, C. / Sollid, L.M. | ||||||
![]() | ![]() Title: Structural basis for HLA-DQ2-mediated presentation of gluten epitopes in celiac disease Authors: Kim, C.-Y. / Quarsten, H. / Bergseng, E. / Khosla, C. / Sollid, L.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.9 KB | Display | ![]() |
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PDB format | ![]() | 134 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 405.3 KB | Display | ![]() |
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Full document | ![]() | 416.3 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21752.373 Da / Num. of mol.: 2 / Fragment: residues (-1)-191 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 23114.023 Da / Num. of mol.: 2 / Fragment: residues 1-198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1328.509 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.16 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: sodium acetate, ammonium acetate, ammonium sulfate, ethylene glycol, PEG 3350, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→69 Å / Num. obs: 44458 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 93.9 % / Num. measured all: 288797 / Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS % possible obs: 76.5 % / Num. unique obs: 1677 / Num. measured obs: 4689 / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.182 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.22→69 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Num. reflection obs: 38843 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.348 / Rfactor Rwork: 0.294 |