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Yorodumi- PDB-5hhv: Inhibiting complex IL-17A and IL-17RA interactions with a linear ... -
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-Basic information
Entry | Database: PDB / ID: 5hhv | ||||||
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Title | Inhibiting complex IL-17A and IL-17RA interactions with a linear peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM/INHIBITOR / IL-17 / inflammation / inhibitor / complex crystal structure / IMMUNE SYSTEM-INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / cell death ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / cell death / interleukin-17-mediated signaling pathway / positive regulation of bicellular tight junction assembly / fibroblast activation / positive regulation of cytokine production involved in inflammatory response / positive regulation of osteoclast differentiation / keratinocyte proliferation / defense response to fungus / cellular response to interleukin-1 / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / cytokine activity / response to wounding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cell-cell signaling / gene expression / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / immune response / inflammatory response / protein heterodimerization activity / external side of plasma membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Liu, S. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Inhibiting complex IL-17A and IL-17RA interactions with a linear peptide. Authors: Liu, S. / Desharnais, J. / Sahasrabudhe, P.V. / Jin, P. / Li, W. / Oates, B.D. / Shanker, S. / Banker, M.E. / Chrunyk, B.A. / Song, X. / Feng, X. / Griffor, M. / Jimenez, J. / Chen, G. / ...Authors: Liu, S. / Desharnais, J. / Sahasrabudhe, P.V. / Jin, P. / Li, W. / Oates, B.D. / Shanker, S. / Banker, M.E. / Chrunyk, B.A. / Song, X. / Feng, X. / Griffor, M. / Jimenez, J. / Chen, G. / Tumelty, D. / Bhat, A. / Bradshaw, C.W. / Woodnutt, G. / Lappe, R.W. / Thorarensen, A. / Qiu, X. / Withka, J.M. / Wood, L.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hhv.cif.gz | 224 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hhv.ent.gz | 178.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/5hhv ftp://data.pdbj.org/pub/pdb/validation_reports/hh/5hhv | HTTPS FTP |
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-Related structure data
Related structure data | 5hhxC 2vxsS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assemble of the complex consists two IL-17A monomer forming a dimer, two Fab binding to IL-17A dimer and two peptide interacting with IL-17A |
-Components
#1: Protein | Mass: 14235.937 Da / Num. of mol.: 2 / Fragment: UNP residues 34-155 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16552 #2: Antibody | | Mass: 25053.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #3: Protein/peptide | | Mass: 1849.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) #4: Antibody | | Mass: 23006.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #5: 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: 2.02 Å3/Da / Density % sol: 39.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: .02 mM CdCl2, 0.02 M MgCl2, 0.02 M NiCl2, 0.1 M NaOAc pH=4.2-4.9, and 24-28 % PEG MME 2000 PH range: 4.2-4.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→95.43 Å / Num. obs: 32509 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 56.29 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.2→2.46 Å / Redundancy: 8 % / Rmerge(I) obs: 0.149 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VXS Resolution: 2.2→95.43 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.222 / SU Rfree Blow DPI: 0.183 / SU Rfree Cruickshank DPI: 0.188
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Displacement parameters | Biso mean: 67.38 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.2→95.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.27 Å / Total num. of bins used: 16
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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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