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Yorodumi- PDB-4o9h: Structure of Interleukin-6 in complex with a Camelid Fab fragment -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o9h | ||||||
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Title | Structure of Interleukin-6 in complex with a Camelid Fab fragment | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IL6: all alpha protein / Fab: all beta protein | ||||||
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) Llama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||
Authors | Klarenbeek, A. / Blanchetot, C. / Schragel, G. / Sadi, A.S. / Ongenae, N. / Hemrika, W. / Wijdenes, J. / Spinelli, S. / Desmyter, A. / Cambillau, C. ...Klarenbeek, A. / Blanchetot, C. / Schragel, G. / Sadi, A.S. / Ongenae, N. / Hemrika, W. / Wijdenes, J. / Spinelli, S. / Desmyter, A. / Cambillau, C. / Hultberg, A. / Kretz-rommel, A. / Dreier, T. / De haard, H.J.W. / Roovers, R.C. | ||||||
Citation | Journal: To be Published Title: Combining residues of naturally-occurring Camelid somatic affinity variants yields ultra-potent human therapeutic IL-6 antibodies Authors: Klarenbeek, A. / Blanchetot, C. / Schragel, G. / Sadi, A.S. / Ongenae, N. / Hemrika, W. / Wijdenes, J. / Spinelli, S. / Desmyter, A. / Cambillau, C. / Hultberg, A. / Kretz-Rommel, A. / ...Authors: Klarenbeek, A. / Blanchetot, C. / Schragel, G. / Sadi, A.S. / Ongenae, N. / Hemrika, W. / Wijdenes, J. / Spinelli, S. / Desmyter, A. / Cambillau, C. / Hultberg, A. / Kretz-Rommel, A. / Dreier, T. / De haard, H.J.W. / Roovers, R.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o9h.cif.gz | 226.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o9h.ent.gz | 189 KB | Display | PDB format |
PDBx/mmJSON format | 4o9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o9h_validation.pdf.gz | 441.6 KB | Display | wwPDB validaton report |
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Full document | 4o9h_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 4o9h_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 4o9h_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/4o9h ftp://data.pdbj.org/pub/pdb/validation_reports/o9/4o9h | 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: 21137.156 Da / Num. of mol.: 1 / Fragment: UNP residues 28-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL6, IFNB2 / Production host: mammalia (mammals) / References: UniProt: P05231 |
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#2: Antibody | Mass: 23504.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Llama glama (llama) / Production host: mammalia (mammals) |
#3: Antibody | Mass: 22529.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Llama glama (llama) / Production host: mammalia (mammals) |
#4: Water | ChemComp-HOH / |
Sequence details | IN THIS STRUCTURE, THE SEQUENCES OF THE H AND L CHAINS WERE NOT AVAILABLE AT THE UNIPROT ...IN THIS STRUCTURE, THE SEQUENCES OF THE H AND L CHAINS WERE NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.3 % |
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Crystal grow | Temperature: 277 K / pH: 5.5 Details: 2M Ammonium sulfate, 0.15M Na citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2010 Details: KIRKPATRICK-BAEZ PAIR OF BI- MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL |
Radiation | Monochromator: KIRKPATRICK-BAEZ PAIR OF BI- MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→45 Å / Num. obs: 28984 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 54.17 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.42→2.48 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→38.65 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.862 / SU R Cruickshank DPI: 0.334 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 65.51 Å2
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Refine analyze | Luzzati coordinate error obs: 0.396 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→38.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.42→2.5 Å / Total num. of bins used: 15
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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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