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Yorodumi- PDB-4ni7: Crystal structure of human interleukin 6 in complex with a modifi... -
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-Basic information
Entry | Database: PDB / ID: 4ni7 | ||||||
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Title | Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025) | ||||||
Components |
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Keywords | CYTOKINE/DNA / Interleukin-6 / CYTOKINE-DNA complex | ||||||
Function / homology | Function and homology information positive regulation of interleukin-21 production / regulation of astrocyte activation / glucagon secretion / regulation of glucagon secretion / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / T follicular helper cell differentiation / germinal center B cell differentiation ...positive regulation of interleukin-21 production / regulation of astrocyte activation / glucagon secretion / regulation of glucagon secretion / hepatic immune response / negative regulation of interleukin-1-mediated signaling pathway / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / T follicular helper cell differentiation / germinal center B cell differentiation / interleukin-6 receptor complex / positive regulation of extracellular matrix disassembly / positive regulation of receptor signaling pathway via STAT / positive regulation of apoptotic DNA fragmentation / response to peptidoglycan / positive regulation of type B pancreatic cell apoptotic process / regulation of microglial cell activation / hepatocyte proliferation / neutrophil apoptotic process / interleukin-6 receptor binding / negative regulation of collagen biosynthetic process / inflammatory response to wounding / T-helper 17 cell lineage commitment / positive regulation of T-helper 2 cell cytokine production / positive regulation of B cell activation / endocrine pancreas development / positive regulation of acute inflammatory response / regulation of neuroinflammatory response / vascular endothelial growth factor production / negative regulation of chemokine production / positive regulation of neuroinflammatory response / positive regulation of leukocyte chemotaxis / positive regulation of platelet aggregation / positive regulation of cytokine production involved in inflammatory response / neutrophil mediated immunity / negative regulation of lipid storage / negative regulation of bone resorption / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / positive regulation of immunoglobulin production / interleukin-6-mediated signaling pathway / maintenance of blood-brain barrier / Interleukin-6 signaling / negative regulation of fat cell differentiation / MAPK3 (ERK1) activation / monocyte chemotaxis / positive regulation of interleukin-17 production / Interleukin-10 signaling / MAPK1 (ERK2) activation / regulation of insulin secretion / positive regulation of glial cell proliferation / positive regulation of interleukin-10 production / humoral immune response / Transcriptional Regulation by VENTX / positive regulation of vascular endothelial growth factor production / regulation of angiogenesis / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / positive regulation of chemokine production / positive regulation of T cell proliferation / response to glucocorticoid / positive regulation of tyrosine phosphorylation of STAT protein / liver regeneration / positive regulation of smooth muscle cell proliferation / positive regulation of interleukin-1 beta production / response to activity / cytokine activity / acute-phase response / positive regulation of interleukin-8 production / positive regulation of translation / Post-translational protein phosphorylation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of DNA-binding transcription factor activity / growth factor activity / platelet activation / cellular response to virus / negative regulation of neurogenesis / cytokine-mediated signaling pathway / cellular response to hydrogen peroxide / neuron cellular homeostasis / ADORA2B mediated anti-inflammatory cytokines production / positive regulation of interleukin-6 production / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-serine phosphorylation / positive regulation of tumor necrosis factor production / neuron projection development / glucose homeostasis / Senescence-Associated Secretory Phenotype (SASP) / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / defense response to virus / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / inflammatory response / positive regulation of apoptotic process / negative regulation of cell population proliferation / endoplasmic reticulum lumen / positive regulation of cell population proliferation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD WITH molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Davies, D. / Edwards, T. / Gelinas, A. / Jarvis, T. / Clifton, M.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Crystal structure of interleukin-6 in complex with a modified nucleic Acid ligand. Authors: Gelinas, A.D. / Davies, D.R. / Edwards, T.E. / Rohloff, J.C. / Carter, J.D. / Zhang, C. / Gupta, S. / Ishikawa, Y. / Hirota, M. / Nakaishi, Y. / Jarvis, T.C. / Janjic, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ni7.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ni7.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ni7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ni7_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 4ni7_full_validation.pdf.gz | 459.1 KB | Display | |
Data in XML | 4ni7_validation.xml.gz | 12 KB | Display | |
Data in CIF | 4ni7_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/4ni7 ftp://data.pdbj.org/pub/pdb/validation_reports/ni/4ni7 | HTTPS FTP |
-Related structure data
Related structure data | 4ni9C 1il6S S: Starting model for refinement C: citing same article (ref.) |
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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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Details | BIOMOLECULE: NULL SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. REMARK: MONOMER |
-Components
#1: Protein | Mass: 21137.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL6, IFNB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P05231 | ||
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#2: DNA chain | Mass: 11402.860 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 31% PEG 3350, 180 mM LiNO3, 100 mM Sodium Acetate (pH 5.5), 2.5% Hexamine Cobalt Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.03318 / Wavelength: 1.03318 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03318 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.4 Å / Num. obs: 11411 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 65.61 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.89 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD WITH molecular replacement Starting model: PDB ENTRY 1IL6 Resolution: 2.4→43.5 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 14.87 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→43.5 Å
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