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- PDB-4ov5: Structure of HLA-DR1 with a bound peptide with non-optimal alanin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ov5 | ||||||
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Title | Structure of HLA-DR1 with a bound peptide with non-optimal alanine in the P1 pocket | ||||||
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![]() | IMMUNE SYSTEM / Ig-like domain | ||||||
Function / homology | ![]() regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / 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 ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / 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 / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / transport vesicle membrane / T cell mediated cytotoxicity directed against tumor cell target / intermediate filament / positive regulation of memory T cell activation / TAP complex binding / polysaccharide binding / T-helper 1 type immune response / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of exogenous peptide antigen via MHC class I / positive regulation of insulin secretion involved in cellular response to glucose stimulus / endoplasmic reticulum exit site / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Generation of second messenger molecules / immunological synapse / TAP binding / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / epidermis development / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / T cell mediated cytotoxicity / structural constituent of cytoskeleton / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / cognition / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Interferon alpha/beta signaling / positive regulation of type II interferon production / Downstream TCR signaling / positive regulation of T cell activation / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / defense response to Gram-positive bacterium / positive regulation of protein phosphorylation / immune response / lysosomal membrane / external side of plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Trenh, P. / Yin, L. / Stern, L.J. | ||||||
![]() | ![]() Title: Susceptibility to HLA-DM Protein Is Determined by a Dynamic Conformation of Major Histocompatibility Complex Class II Molecule Bound with Peptide. Authors: Yin, L. / Trenh, P. / Guce, A. / Wieczorek, M. / Lange, S. / Sticht, J. / Jiang, W. / Bylsma, M. / Mellins, E.D. / Freund, C. / Stern, L.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 467.1 KB | Display | ![]() |
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PDB format | ![]() | 382.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 541.9 KB | Display | ![]() |
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Full document | ![]() | 558.3 KB | Display | |
Data in XML | ![]() | 80.9 KB | Display | |
Data in CIF | ![]() | 112.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1aqdS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21155.904 Da / Num. of mol.: 6 Fragment: Secreted extracellular domain (UNP residues 26-207) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 22080.664 Da / Num. of mol.: 6 Fragment: Secreted extracellular domain (UNP residues 30-219) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 1628.811 Da / Num. of mol.: 6 / Fragment: peptide (UNP residues 128-141) / Mutation: W1A, Q9L / Source method: obtained synthetically / Source: (synth.) ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 4% PEG4000, 10% ethylene glycol, 100 mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2012 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.199→46 Å / Num. all: 140622 / Num. obs: 140577 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.44 / Redundancy: 2.5 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 16.09 |
Reflection shell | Resolution: 2.199→2.24 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 1.44 / Num. unique all: 6124 / Rsym value: 0.477 / % possible all: 81.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AQD Resolution: 2.199→41.511 Å / SU ML: 0.32 / σ(F): 1.39 / Phase error: 26.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.199→41.511 Å
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Refine LS restraints |
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LS refinement shell |
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