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- PDB-7z0q: MHC-II dynamics are maintained in HLA-DR allotypes to ensure cata... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7z0q | ||||||
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Title | MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange | ||||||
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![]() | IMMUNE SYSTEM / HLA-DRB1*0701 / CLIP peptide / MHCII | ||||||
Function / homology | ![]() myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane ...myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / immunological synapse / PD-1 signaling / T cell receptor binding / 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 / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / 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 / early endosome membrane / adaptive immune response / lysosome / endosome membrane / immune response / lysosomal membrane / Golgi membrane / cell surface / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Roske, Y. / Abualrous, E.T. / Freund, C. | ||||||
Funding support | 1items
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![]() | ![]() Title: MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange. Authors: Abualrous, E.T. / Stolzenberg, S. / Sticht, J. / Wieczorek, M. / Roske, Y. / Gunther, M. / Dahn, S. / Boesen, B.B. / Calvo, M.M. / Biese, C. / Kuppler, F. / Medina-Garcia, A. / Alvaro- ...Authors: Abualrous, E.T. / Stolzenberg, S. / Sticht, J. / Wieczorek, M. / Roske, Y. / Gunther, M. / Dahn, S. / Boesen, B.B. / Calvo, M.M. / Biese, C. / Kuppler, F. / Medina-Garcia, A. / Alvaro-Benito, M. / Hofer, T. / Noe, F. / Freund, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.4 KB | Display | ![]() |
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PDB format | ![]() | 137.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.4 KB | Display | ![]() |
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Full document | ![]() | 469.6 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yx9C ![]() 7yxbC ![]() 4x5xS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22207.057 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Protein | Mass: 22967.658 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#3: Protein/peptide | Mass: 1847.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.15M Sodiummalonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→38.71 Å / Num. obs: 28123 / % possible obs: 98.6 % / Redundancy: 4 % / Biso Wilson estimate: 61.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.0763 / Net I/σ(I): 12.06 |
Reflection shell | Resolution: 2.1→2.175 Å / Num. unique obs: 2850 / CC1/2: 0.44 / Rrim(I) all: 2.559 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 4X5X Resolution: 2.1→38.71 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.198 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.172
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Displacement parameters | Biso max: 229.64 Å2 / Biso mean: 92.89 Å2 / Biso min: 30 Å2
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Refine analyze | Luzzati coordinate error obs: 0.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→38.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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