+Open data
-Basic information
Entry | Database: PDB / ID: 3vq1 | |||||||||
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Title | Crystal structure of mouse TLR4/MD-2/lipid IVa complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Leucine rich repeat MD-2 related lipid recognition / receptor innate immunity / lipid binding / glycosylation / secreted | |||||||||
Function / homology | Function and homology information MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / TRIF-mediated programmed cell death / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / Heme signaling / Regulation of TLR by endogenous ligand / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex ...MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / TRIF-mediated programmed cell death / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / Heme signaling / Regulation of TLR by endogenous ligand / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / lipopolysaccharide immune receptor activity / Toll-like receptor 4 binding / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / IKK complex recruitment mediated by RIP1 / lipopolysaccharide receptor complex / innate immune response-activating signaling pathway / mast cell activation / positive regulation of matrix metallopeptidase secretion / detection of lipopolysaccharide / regulation of dendritic cell cytokine production / intestinal epithelial structure maintenance / positive regulation of lymphocyte proliferation / negative regulation of interleukin-23 production / positive regulation of stress-activated MAPK cascade / lymphocyte proliferation / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / wound healing involved in inflammatory response / B cell proliferation involved in immune response / leukotriene metabolic process / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of interleukin-1 production / positive regulation of lipopolysaccharide-mediated signaling pathway / macrophage activation / microglia differentiation / astrocyte development / TRIF-dependent toll-like receptor signaling pathway / response to fatty acid / activation of NF-kappaB-inducing kinase activity / positive regulation of macrophage activation / regulation of tumor necrosis factor production / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of interleukin-17 production / positive regulation of cytokine production involved in inflammatory response / NADP+ nucleosidase activity / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of MHC class II biosynthetic process / positive regulation of platelet activation / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of cold-induced thermogenesis / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / positive regulation of reactive oxygen species biosynthetic process / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / phagocytic cup / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of interleukin-13 production / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / B cell proliferation / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of interferon-alpha production / detection of temperature stimulus involved in sensory perception of pain / cellular response to lipoteichoic acid / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / stress-activated MAPK cascade / detection of mechanical stimulus involved in sensory perception of pain / phosphatidylinositol 3-kinase binding / phagocytosis / positive regulation of B cell proliferation / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / ERK1 and ERK2 cascade / ruffle / nitric oxide biosynthetic process / activation of innate immune response / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / neurogenesis / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / lipopolysaccharide binding / response to bacterium / positive regulation of smooth muscle cell proliferation / positive regulation of JNK cascade / microglial cell activation / positive regulation of MAP kinase activity / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Ohto, U. / Shimizu, T. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural basis of species-specific endotoxin sensing by innate immune receptor TLR4/MD-2 Authors: Ohto, U. / Fukase, K. / Miyake, K. / Shimizu, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vq1.cif.gz | 574.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vq1.ent.gz | 473.9 KB | Display | PDB format |
PDBx/mmJSON format | 3vq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/3vq1 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/3vq1 | HTTPS FTP |
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-Related structure data
Related structure data | 3vq2C 2z64S 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
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 68713.336 Da / Num. of mol.: 2 / Fragment: UNP residues 22-627 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tlr4 / Cell (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: Q9QUK6 #2: Protein | Mass: 16627.900 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Md2 / Cell (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: Q9JHF9 |
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-Sugars , 2 types, 5 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 3 types, 41 molecules
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 15% PEG4000, 0.2M Na acetate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 2, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→116 Å / Num. obs: 54275 / Rsym value: 0.147 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z64 Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.88 / SU B: 27.394 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.947 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.119 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.697→2.767 Å / Total num. of bins used: 20
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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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