+Open data
-Basic information
Entry | Database: PDB / ID: 8b7w | ||||||
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Title | Complex IL-17A/anti-IL-17A-76 | ||||||
Components |
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Keywords | IMMUNE SYSTEM/INHIBITOR / interleukin 17A in complex with VHH domain / netakimab / crystal structure. / immune system / inhibitor / 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 / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production ...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 / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / positive regulation of bicellular tight junction assembly / fibroblast activation / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / 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 / inflammatory response / immune 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 | Lama glama (llama) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Kostareva, O.S. / Svoeglazova, A. / Kolyadenko, I.A. / Dzhus, U.F. / Tishchenko, S.V. / Gabdulkhakov, A.G. | ||||||
Funding support | 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Two Epitope Regions Revealed in the Complex of IL-17A and Anti-IL-17A V H H Domain. Authors: Kostareva, O. / Svoeglazova, A. / Kolyadenko, I. / Nikulin, A. / Evdokimov, S. / Dzhus, U. / Gabdulkhakov, A. / Tishchenko, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b7w.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b7w.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 8b7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b7w_validation.pdf.gz | 574.2 KB | Display | wwPDB validaton report |
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Full document | 8b7w_full_validation.pdf.gz | 578.3 KB | Display | |
Data in XML | 8b7w_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 8b7w_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/8b7w ftp://data.pdbj.org/pub/pdb/validation_reports/b7/8b7w | HTTPS FTP |
-Related structure data
Related structure data | 4hr9S 6rbbS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody / Protein , 2 types, 2 molecules HC
#1: Antibody | Mass: 13261.681 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
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#2: Protein | Mass: 14120.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16552 |
-Non-polymers , 4 types, 25 molecules
#3: Chemical | ChemComp-GOL / |
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#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-SO4 / |
#6: Water | ChemComp-HOH / |
-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: 2.82 Å3/Da / Density % sol: 56.41 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / Details: 1.05 M NaCl, 7% v/v ethanol, 30% glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 7466 / % possible obs: 98.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 73.32 Å2 / CC1/2: 0.96 / Rrim(I) all: 0.27 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.85→2.92 Å / Mean I/σ(I) obs: 1.58 / Num. unique obs: 538 / CC1/2: 0.46 / Rrim(I) all: 1.97 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HR9, 6RBB Resolution: 2.85→40.17 Å / SU ML: 0.3313 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.2717 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.04 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→40.17 Å
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Refine LS restraints |
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LS refinement shell |
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