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Yorodumi- PDB-4cni: Crystal structure of the Fab portion of Olokizumab in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 4cni | ||||||
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Title | Crystal structure of the Fab portion of Olokizumab in complex with IL- 6 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CDP6038 / INTERLEUKIN 6 | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Shaw, S. / Bourne, T. / Meier, C. / Carrington, B. / Gelinas, R. / Henry, A. / Popplewell, A. / Adams, R. / Baker, T. / Rapecki, S. ...Shaw, S. / Bourne, T. / Meier, C. / Carrington, B. / Gelinas, R. / Henry, A. / Popplewell, A. / Adams, R. / Baker, T. / Rapecki, S. / Marshall, D. / Neale, H. / Lawson, A. | ||||||
Citation | Journal: Mabs / Year: 2014 Title: Discovery and Characterization of Olokizumab: A Humanized Antibody Targeting Interleukin-6 and Neutralizing Gp130-Signaling. Authors: Shaw, S. / Bourne, T. / Meier, C. / Carrington, B. / Gelinas, R. / Henry, A. / Popplewell, A. / Adams, R. / Baker, T. / Rapecki, S. / Marshall, D. / Moore, A. / Neale, H. / Lawson, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cni.cif.gz | 275.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cni.ent.gz | 229.5 KB | Display | PDB format |
PDBx/mmJSON format | 4cni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/4cni ftp://data.pdbj.org/pub/pdb/validation_reports/cn/4cni | 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
-Protein , 1 types, 2 molecules CD
#3: Protein | Mass: 19670.518 Da / Num. of mol.: 2 / Fragment: RESIDUES 41-212 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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-Antibody , 2 types, 4 molecules AHBL
#1: Antibody | Mass: 23940.588 Da / Num. of mol.: 2 / Fragment: FAB PORTION Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY #2: Antibody | Mass: 23280.766 Da / Num. of mol.: 2 / Fragment: FAB PORTION Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY |
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-Non-polymers , 3 types, 1594 molecules
#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: 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: 4.84 Å3/Da / Density % sol: 74.58 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35 Å / Num. obs: 126842 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.2 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.971 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Displacement parameters | Biso mean: 22.986 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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