+Open data
-Basic information
Entry | Database: PDB / ID: 4y19 | |||||||||
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Title | immune complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / TCR MHC | |||||||||
Function / homology | Function and homology information 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 type II interferon production / negative regulation of respiratory burst involved in inflammatory response / 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 / negative regulation of lipid catabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / 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 / detection of bacterium / negative regulation of T cell proliferation / 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 / acute-phase response / Regulation of insulin secretion / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / lumenal side of endoplasmic reticulum membrane / positive regulation of cell differentiation / protein tetramerization / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / wound healing / clathrin-coated endocytic vesicle membrane / insulin receptor binding / regulation of synaptic plasticity / ER to Golgi transport vesicle membrane / negative regulation of protein catabolic process Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Beringer, D.X. / Petersen, J. / Reid, H.H. / Rossjohn, J. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Nat.Immunol. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y19.cif.gz | 355.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y19.ent.gz | 286.8 KB | Display | PDB format |
PDBx/mmJSON format | 4y19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y19_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4y19_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4y19_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 4y19_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/4y19 ftp://data.pdbj.org/pub/pdb/validation_reports/y1/4y19 | HTTPS FTP |
-Related structure data
Related structure data | 4y1aC 1bd2S 4g8fS 4mdiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 21919.594 Da / Num. of mol.: 1 / Fragment: UNP residues 26-206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P01903 |
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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.) Homo sapiens (human) / Gene: HLA-DRB1 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P13760, UniProt: P01911*PLUS |
-Protein/peptide / Antibody / Protein , 3 types, 3 molecules CDE
#3: Protein/peptide | Mass: 1655.895 Da / Num. of mol.: 1 / Fragment: UNP residues 75-90 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308 |
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#4: Antibody | Mass: 23315.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 |
#5: Protein | Mass: 27527.889 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 |
-Sugars , 2 types, 2 molecules
#6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#7: 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 |
-Non-polymers , 2 types, 309 molecules
#8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES pH 6.0, 2 M ammonium sulfate and 0.2 M sodium malonate |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→36.6 Å / Num. obs: 47168 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 41.59 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G8F, 1BD2, 4MDI Resolution: 2.5→36.6 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.246 / SU Rfree Blow DPI: 0.188 / SU Rfree Cruickshank DPI: 0.189
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Displacement parameters | Biso mean: 34.62 Å2
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Refine analyze | Luzzati coordinate error obs: 0.262 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→36.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Total num. of bins used: 20
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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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