+Open data
-Basic information
Entry | Database: PDB / ID: 7dc8 | ||||||
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Title | Crystal structure of Switch Ab Fab and hIL6R in complex with ATP | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTIBODY / COMPLEX / FAB / CYTOKINE | ||||||
Function / homology | Function and homology information ciliary neurotrophic factor binding / interleukin-6 receptor activity / interleukin-6 binding / hepatic immune response / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor-mediated signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-6 receptor complex / negative regulation of collagen biosynthetic process ...ciliary neurotrophic factor binding / interleukin-6 receptor activity / interleukin-6 binding / hepatic immune response / interleukin-11 receptor activity / interleukin-11 binding / ciliary neurotrophic factor-mediated signaling pathway / ciliary neurotrophic factor receptor complex / interleukin-6 receptor complex / negative regulation of collagen biosynthetic process / : / T-helper 17 cell lineage commitment / endocrine pancreas development / positive regulation of glomerular mesangial cell proliferation / negative regulation of interleukin-8 production / vascular endothelial growth factor production / positive regulation of leukocyte chemotaxis / neutrophil mediated immunity / cytokine receptor activity / interleukin-6-mediated signaling pathway / Interleukin-6 signaling / MAPK3 (ERK1) activation / monocyte chemotaxis / MAPK1 (ERK2) activation / positive regulation of osteoblast differentiation / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of smooth muscle cell proliferation / response to cytokine / acute-phase response / Transcriptional regulation of granulopoiesis / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / positive regulation of peptidyl-tyrosine phosphorylation / Potential therapeutics for SARS / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / receptor complex / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / apical plasma membrane / external side of plasma membrane / positive regulation of cell population proliferation / enzyme binding / protein homodimerization activity / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.757 Å | ||||||
Authors | Kadono, S. / Fukami, T.A. / Kawauchi, H. / Torizawa, T. / Mimoto, F. | ||||||
Citation | Journal: Cell Rep / Year: 2020 Title: Exploitation of Elevated Extracellular ATP to Specifically Direct Antibody to Tumor Microenvironment. Authors: Mimoto, F. / Tatsumi, K. / Shimizu, S. / Kadono, S. / Haraya, K. / Nagayasu, M. / Suzuki, Y. / Fujii, E. / Kamimura, M. / Hayasaka, A. / Kawauchi, H. / Ohara, K. / Matsushita, M. / Baba, T. ...Authors: Mimoto, F. / Tatsumi, K. / Shimizu, S. / Kadono, S. / Haraya, K. / Nagayasu, M. / Suzuki, Y. / Fujii, E. / Kamimura, M. / Hayasaka, A. / Kawauchi, H. / Ohara, K. / Matsushita, M. / Baba, T. / Susumu, H. / Sakashita, T. / Muraoka, T. / Aso, K. / Katada, H. / Tanaka, E. / Nakagawa, K. / Hasegawa, M. / Ayabe, M. / Yamamoto, T. / Tanba, S. / Ishiguro, T. / Kamikawa, T. / Nambu, T. / Kibayashi, T. / Azuma, Y. / Tomii, Y. / Kato, A. / Ozeki, K. / Murao, N. / Endo, M. / Kikuta, J. / Kamata-Sakurai, M. / Ishii, M. / Hattori, K. / Igawa, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dc8.cif.gz | 247 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dc8.ent.gz | 193 KB | Display | PDB format |
PDBx/mmJSON format | 7dc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dc8_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7dc8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7dc8_validation.xml.gz | 43.1 KB | Display | |
Data in CIF | 7dc8_validation.cif.gz | 59.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/7dc8 ftp://data.pdbj.org/pub/pdb/validation_reports/dc/7dc8 | HTTPS FTP |
-Related structure data
Related structure data | 7dc7C 1n26S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules CF
#3: Protein | Mass: 25001.795 Da / Num. of mol.: 2 / Mutation: C193S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL6R / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P08887 |
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-Antibody , 2 types, 4 molecules ADBE
#1: Antibody | Mass: 22824.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) #2: Antibody | Mass: 24744.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) |
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-Non-polymers , 3 types, 75 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.51 Å3/Da / Density % sol: 50.9 % / Mosaicity: 0.1 ° |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7.5 Details: 0.06 M Tris, 12.0 %(w/v) Polyethylene glycol 1500, 0.06 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.75→92.81 Å / Num. obs: 38295 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.03 / Rrim(I) all: 0.111 / Net I/σ(I): 20 / Num. measured all: 510514 / Scaling rejects: 9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N26 Resolution: 2.757→90.091 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.46 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.4 Å2 / Biso mean: 58.3162 Å2 / Biso min: 22.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.757→90.091 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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