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Open data
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Basic information
Entry | Database: PDB / ID: 4y1a | |||||||||
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Title | immune complex | |||||||||
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![]() | IMMUNE SYSTEM / TCR MHC | |||||||||
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 / intermediate filament / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / polysaccharide binding / T-helper 1 type immune response / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / alpha-beta T cell activation / humoral immune response / macrophage differentiation / negative regulation of respiratory burst involved in inflammatory response / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / PD-1 signaling / Synthesis, secretion, and deacylation of Ghrelin / epidermis development / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / T cell receptor binding / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / negative regulation of T cell proliferation / detection of bacterium / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / negative regulation of inflammatory response to antigenic stimulus / Insulin receptor recycling / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / MHC class II antigen presentation / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / trans-Golgi network membrane / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / Regulation of insulin secretion / acute-phase response / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / lumenal side of endoplasmic reticulum membrane / positive regulation of cell differentiation / negative regulation of proteolysis / protein tetramerization / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / clathrin-coated endocytic vesicle membrane / wound healing / insulin receptor binding / regulation of synaptic plasticity / ER to Golgi transport vesicle membrane / negative regulation of protein catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Beringer, D.X. / Vivian, J.P. / Reid, H.H. / Rossjohn, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: T cell receptor reversed polarity recognition of a self-antigen major histocompatibility complex. Authors: Beringer, D.X. / Kleijwegt, F.S. / Wiede, F. / van der Slik, A.R. / Loh, K.L. / Petersen, J. / Dudek, N.L. / Duinkerken, G. / Laban, S. / Joosten, A. / Vivian, J.P. / Chen, Z. / Uldrich, A.P. ...Authors: Beringer, D.X. / Kleijwegt, F.S. / Wiede, F. / van der Slik, A.R. / Loh, K.L. / Petersen, J. / Dudek, N.L. / Duinkerken, G. / Laban, S. / Joosten, A. / Vivian, J.P. / Chen, Z. / Uldrich, A.P. / Godfrey, D.I. / McCluskey, J. / Price, D.A. / Radford, K.J. / Purcell, A.W. / Nikolic, T. / Reid, H.H. / Tiganis, T. / Roep, B.O. / Rossjohn, 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 | ![]() | 175.1 KB | Display | ![]() |
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PDB format | ![]() | 139.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 704.5 KB | Display | ![]() |
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Full document | ![]() | 714.6 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 21084.826 Da / Num. of mol.: 1 / Fragment: UNP residues 26-206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 23224.617 Da / Num. of mol.: 1 / Fragment: UNP residues 30-219 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein/peptide / Antibody / Protein / Sugars , 4 types, 4 molecules CDE
#3: Protein/peptide | Mass: 1655.895 Da / Num. of mol.: 1 / Fragment: UNP residues 75-90 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#4: Antibody | Mass: 23227.779 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 27440.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.99 Å3/Da / Density % sol: 69.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: BisTris, ammonium sulfate and pentaerythritol ethoxylate (3/4 EO/OH) |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. obs: 13145 / % possible obs: 98.5 % / Redundancy: 5 % / Net I/σ(I): 5.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 4→47.292 Å
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Refine LS restraints |
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LS refinement shell |
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