+Open data
-Basic information
Entry | Database: PDB / ID: 1alu | ||||||
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Title | HUMAN INTERLEUKIN-6 | ||||||
Components | INTERLEUKIN-6Interleukin 6 | ||||||
Keywords | CYTOKINE / INTERLEUKIN / RECEPTOR / SIGNALING / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information positive regulation of interleukin-21 production / regulation of astrocyte activation / glucagon secretion / negative regulation of interleukin-1-mediated signaling pathway / hepatic immune response / regulation of glucagon secretion / 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 / negative regulation of interleukin-1-mediated signaling pathway / hepatic immune response / regulation of glucagon secretion / regulation of vascular endothelial growth factor production / negative regulation of primary miRNA processing / T follicular helper cell differentiation / germinal center B cell differentiation / regulation of microglial cell activation / interleukin-6 receptor complex / positive regulation of extracellular matrix disassembly / positive regulation of receptor signaling pathway via STAT / positive regulation of type B pancreatic cell apoptotic process / positive regulation of apoptotic DNA fragmentation / response to peptidoglycan / 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 / neutrophil mediated immunity / positive regulation of cytokine production involved in inflammatory response / negative regulation of bone resorption / CD163 mediating an anti-inflammatory response / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of fat cell differentiation / maintenance of blood-brain barrier / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / positive regulation of interleukin-17 production / MAPK3 (ERK1) activation / Interleukin-10 signaling / monocyte chemotaxis / MAPK1 (ERK2) activation / positive regulation of interleukin-10 production / regulation of insulin secretion / humoral immune response / negative regulation of lipid storage / positive regulation of immunoglobulin production / Transcriptional Regulation by VENTX / positive regulation of vascular endothelial growth factor production / positive regulation of epithelial to mesenchymal transition / positive regulation of osteoblast differentiation / regulation of angiogenesis / positive regulation of chemokine production / positive regulation of glial cell proliferation / response to glucocorticoid / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / positive regulation of translation / response to activity / positive regulation of interleukin-1 beta production / cytokine activity / liver regeneration / positive regulation of interleukin-8 production / Post-translational protein phosphorylation / acute-phase response / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / cellular response to hydrogen peroxide / platelet activation / cellular response to virus / ADORA2B mediated anti-inflammatory cytokines production / negative regulation of neurogenesis / positive regulation of interleukin-6 production / neuron cellular homeostasis / cytokine-mediated signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / positive regulation of DNA-binding transcription factor activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / glucose homeostasis / positive regulation of peptidyl-serine phosphorylation / Senescence-Associated Secretory Phenotype (SASP) / defense response to virus / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / inflammatory response / positive regulation of apoptotic process / endoplasmic reticulum lumen / negative regulation of cell population proliferation / positive regulation of cell population proliferation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.9 Å | ||||||
Authors | Somers, W.S. / Stahl, M. / Seehra, J.S. | ||||||
Citation | Journal: EMBO J. / Year: 1997 Title: 1.9 A crystal structure of interleukin 6: implications for a novel mode of receptor dimerization and signaling. Authors: Somers, W. / Stahl, M. / Seehra, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1alu.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1alu.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 1alu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/1alu ftp://data.pdbj.org/pub/pdb/validation_reports/al/1alu | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-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) / Production host: Escherichia coli (E. coli) / References: UniProt: P05231 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-TLA / | #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: 2.17 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||
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Crystal grow | pH: 6.3 Details: PROTEIN AT 15 MG/ML WAS CRYSTALLIZED FROM 1.8M AMMONIUM SULFATE, 300 MM SODIUM POTASSIUM TARTRATE, IN 100MM PH 6.3 SODIUM CITRATE BUFFER. | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→10 Å / Num. obs: 14002 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 5.8 / Rsym value: 0.129 / % possible all: 88.5 |
Reflection | *PLUS Num. measured all: 100519 |
Reflection shell | *PLUS % possible obs: 88.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.213 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |