+Open data
-Basic information
Entry | Database: PDB / ID: 6nig | |||||||||
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Title | Crystal structure of the human TLR2-Diprovocim complex | |||||||||
Components | Toll-like receptor 2,Variable lymphocyte receptor B | |||||||||
Keywords | IMMUNE SYSTEM/AGONIST / Toll-like receptors / innate immune agonist / IMMUNE SYSTEM-AGONIST complex | |||||||||
Function / homology | Function and homology information Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / toll-like receptor TLR6:TLR2 signaling pathway / cellular response to diacyl bacterial lipopeptide / Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / cellular response to bacterial lipopeptide ...Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / toll-like receptor TLR6:TLR2 signaling pathway / cellular response to diacyl bacterial lipopeptide / Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / cellular response to bacterial lipopeptide / negative regulation of synapse assembly / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / lipopolysaccharide immune receptor activity / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / toll-like receptor 2 signaling pathway / positive regulation of matrix metallopeptidase secretion / I-kappaB phosphorylation / nitric oxide metabolic process / central nervous system myelin formation / Toll-like receptor binding / positive regulation of interleukin-18 production / leukotriene metabolic process / Regulation of TLR by endogenous ligand / response to fatty acid / peptidoglycan binding / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / microglia development / MyD88 deficiency (TLR2/4) / negative regulation of phagocytosis / pattern recognition receptor activity / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor signaling pathway / positive regulation of oligodendrocyte differentiation / positive regulation of nitric-oxide synthase biosynthetic process / cellular response to lipoteichoic acid / positive regulation of interleukin-10 production / positive regulation of Wnt signaling pathway / positive regulation of chemokine production / positive regulation of interferon-beta production / positive regulation of interleukin-12 production / secretory granule membrane / response to progesterone / learning / cell projection / positive regulation of interleukin-8 production / lipopolysaccharide binding / microglial cell activation / response to insulin / response to toxic substance / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / phagocytic vesicle membrane / Modulation by Mtb of host immune system / transmembrane signaling receptor activity / positive regulation of tumor necrosis factor production / signaling receptor activity / cell body / amyloid-beta binding / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / defense response to virus / membrane => GO:0016020 / response to hypoxia / receptor complex / defense response to Gram-positive bacterium / immune response / inflammatory response / membrane raft / negative regulation of cell population proliferation / innate immune response / apoptotic process / Neutrophil degranulation / protein-containing complex binding / positive regulation of gene expression / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Eptatretus stoutii (Pacific hagfish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Zhang, H. / Beutler, B.A. / Tomchick, D.R. / Su, L. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J. Med. Chem. / Year: 2019 Title: Structural Basis of TLR2/TLR1 Activation by the Synthetic Agonist Diprovocim. Authors: Su, L. / Wang, Y. / Wang, J. / Mifune, Y. / Morin, M.D. / Jones, B.T. / Moresco, E.M.Y. / Boger, D.L. / Beutler, B. / Zhang, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nig.cif.gz | 951.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nig.ent.gz | 811.5 KB | Display | PDB format |
PDBx/mmJSON format | 6nig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/6nig ftp://data.pdbj.org/pub/pdb/validation_reports/ni/6nig | HTTPS FTP |
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-Related structure data
Related structure data | 6nihC 2z7xS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 65277.645 Da / Num. of mol.: 4 Fragment: TLR (UNP residues 1-507) + linker + VLR (UNP residues 181-248) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus stoutii (Pacific hagfish) Gene: TLR2, TIL4, VLRB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O60603, UniProt: Q2YE02 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: Chemical | ChemComp-KQD / ( #4: Sugar | ChemComp-NAG / #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: 2.72 Å3/Da / Density % sol: 54.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium citrate tribasic, pH 7.0, 0.1 M imidazole, pH 7.5, 18% PEG1900 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 118654 / % possible obs: 94.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 66.79 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.036 / Rrim(I) all: 0.08 / Χ2: 1.464 / Net I/σ(I): 8.2 / Num. measured all: 506871 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z7X Resolution: 2.35→37.761 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.21 / Stereochemistry target values: ML
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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 max: 263.33 Å2 / Biso mean: 93.801 Å2 / Biso min: 42.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→37.761 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24
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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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