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Yorodumi- PDB-4zs7: Structural mimicry of receptor interaction by antagonistic IL-6 a... -
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-Basic information
Entry | Database: PDB / ID: 4zs7 | ||||||
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Title | Structural mimicry of receptor interaction by antagonistic IL-6 antibodies | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Interleukine 6 Complex / Fab fragment / Dromedery | ||||||
Function / homology | Function and homology information positive regulation of interleukin-21 production / regulation of astrocyte activation / glucagon secretion / regulation of glucagon secretion / negative regulation of interleukin-1-mediated signaling pathway / hepatic immune response / 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 / negative regulation of interleukin-1-mediated signaling pathway / hepatic immune response / 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 platelet aggregation / neutrophil mediated immunity / positive regulation of cytokine production involved in inflammatory response / negative regulation of bone resorption / positive regulation of leukocyte chemotaxis / positive regulation of leukocyte adhesion to vascular endothelial cell / CD163 mediating an anti-inflammatory response / positive regulation of immunoglobulin production / maintenance of blood-brain barrier / interleukin-6-mediated signaling pathway / Interleukin-6 signaling / negative regulation of fat cell differentiation / positive regulation of interleukin-17 production / MAPK3 (ERK1) activation / Interleukin-10 signaling / monocyte chemotaxis / MAPK1 (ERK2) activation / regulation of insulin secretion / positive regulation of interleukin-10 production / humoral immune response / negative regulation of lipid storage / 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 T cell proliferation / positive regulation of chemokine production / response to glucocorticoid / positive regulation of glial cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / response to activity / positive regulation of interleukin-1 beta production / cytokine activity / acute-phase response / positive regulation of translation / positive regulation of interleukin-8 production / liver regeneration / Post-translational protein phosphorylation / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / platelet activation / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of neurogenesis / cellular response to hydrogen peroxide / neuron cellular homeostasis / ADORA2B mediated anti-inflammatory cytokines production / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / neuron projection development / positive regulation of peptidyl-serine phosphorylation / 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) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.93 Å | ||||||
Authors | Blanchetot, C. / De Jonge, N. / Desmyter, A. / Ongenae, N. / Hofman, E. / Klarenbeek, A. / Sadi, A. / Hultberg, A. / Kretz-Rommel, A. / Spinelli, S. ...Blanchetot, C. / De Jonge, N. / Desmyter, A. / Ongenae, N. / Hofman, E. / Klarenbeek, A. / Sadi, A. / Hultberg, A. / Kretz-Rommel, A. / Spinelli, S. / Loris, R. / Cambillau, C. / de Haard, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Mimicry of Receptor Interaction by Antagonistic Interleukin-6 (IL-6) Antibodies. Authors: Blanchetot, C. / De Jonge, N. / Desmyter, A. / Ongenae, N. / Hofman, E. / Klarenbeek, A. / Sadi, A. / Hultberg, A. / Kretz-Rommel, A. / Spinelli, S. / Loris, R. / Cambillau, C. / de Haard, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zs7.cif.gz | 214 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zs7.ent.gz | 177.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zs7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zs7_validation.pdf.gz | 446.5 KB | Display | wwPDB validaton report |
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Full document | 4zs7_full_validation.pdf.gz | 465.2 KB | Display | |
Data in XML | 4zs7_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 4zs7_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/4zs7 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/4zs7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19670.518 Da / Num. of mol.: 1 / Fragment: residues 14-184 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: Antibody | Mass: 23822.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Lama glama (llama) |
#3: Antibody | Mass: 22949.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Lama glama (llama) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 53.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 4K, 0.15 M (NH4)2SO4, 0.1 M MES pH 5.5. Took 9 month |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.971 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.971 Å / Relative weight: 1 |
Reflection | Resolution: 2.93→45 Å / Num. obs: 14778 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 45.64 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.93→3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.8 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Resolution: 2.93→44.35 Å / Cor.coef. Fo:Fc: 0.7636 / Cor.coef. Fo:Fc free: 0.7153 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.46
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Displacement parameters | Biso mean: 30.46 Å2
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Refine analyze | Luzzati coordinate error obs: 0.503 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.93→44.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.93→3.17 Å / Total num. of bins used: 7
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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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