+Open data
-Basic information
Entry | Database: PDB / ID: 2z64 | |||||||||
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Title | Crystal structure of mouse TLR4 and mouse MD-2 complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / TLR4 / toll-like receptor / MD-2 / LPS / Disease mutation / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Leucine-rich repeat / Membrane / Transmembrane / Secreted | |||||||||
Function / homology | Function and homology information MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / TRIF-mediated programmed cell death / Toll Like Receptor 4 (TLR4) Cascade / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 ...MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / TRIF-mediated programmed cell death / Toll Like Receptor 4 (TLR4) Cascade / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / 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 / positive regulation of matrix metallopeptidase secretion / lipopolysaccharide receptor complex / innate immune response-activating signaling pathway / regulation of dendritic cell cytokine production / detection of lipopolysaccharide / positive regulation of lymphocyte proliferation / mast cell activation / intestinal epithelial structure maintenance / negative regulation of interleukin-23 production / lymphocyte proliferation / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to oxidised low-density lipoprotein particle stimulus / wound healing involved in inflammatory response / B cell proliferation involved in immune response / leukotriene metabolic process / nucleotide-binding oligomerization domain containing 1 signaling pathway / activation of NF-kappaB-inducing kinase activity / positive regulation of interleukin-1 production / positive regulation of stress-activated MAPK cascade / positive regulation of lipopolysaccharide-mediated signaling pathway / macrophage activation / TRIF-dependent toll-like receptor signaling pathway / positive regulation of interleukin-13 production / astrocyte development / microglia differentiation / response to fatty acid / regulation of tumor necrosis factor production / nucleotide-binding oligomerization domain containing 2 signaling pathway / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of MHC class II biosynthetic process / positive regulation of cytokine production involved in inflammatory response / negative regulation of interleukin-17 production / positive regulation of macrophage activation / positive regulation of platelet activation / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / 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 / positive regulation of NLRP3 inflammasome complex assembly / toll-like receptor signaling pathway / 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 / cellular response to lipoteichoic acid / detection of temperature stimulus involved in sensory perception of pain / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / positive regulation of interferon-alpha production / phagocytic cup / negative regulation of tumor necrosis factor production / negative regulation of type II interferon production / phosphatidylinositol 3-kinase binding / detection of mechanical stimulus involved in sensory perception of pain / phagocytosis / stress-activated MAPK cascade / positive regulation of chemokine production / positive regulation of B cell proliferation / JNK cascade / lipopolysaccharide-mediated signaling pathway / ruffle / nitric oxide biosynthetic process / ERK1 and ERK2 cascade / 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 / positive regulation of JNK cascade / positive regulation of smooth muscle cell proliferation / response to bacterium / 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 / cellular response to mechanical stimulus / 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: 2.84 Å | |||||||||
Authors | Lee, J.-O. / Kim, H.M. / Park, B.S. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2007 Title: Crystal Structure of the TLR4-MD-2 Complex with Bound Endotoxin Antagonist Eritoran Authors: Kim, H.M. / Park, B.S. / Kim, J.-I. / Kim, S.E. / Lee, J. / Oh, S.C. / Enkhbayar, P. / Matsushima, N. / Lee, H. / Yoo, O.J. / Lee, J.-O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z64.cif.gz | 172.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z64.ent.gz | 132.7 KB | Display | PDB format |
PDBx/mmJSON format | 2z64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z64 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z64 | HTTPS FTP |
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-Related structure data
Related structure data | 2z62C 2z63SC 2z65C 2z66C 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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Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Components
-Protein , 2 types, 2 molecules AC
#1: Protein | Mass: 67950.461 Da / Num. of mol.: 1 / Fragment: TLR4, UNP residues 27-625 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tlr4 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi-5 / References: UniProt: Q9QUK6 |
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#2: Protein | Mass: 15510.707 Da / Num. of mol.: 1 / Fragment: MD-2, UNP residues 21-160 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Md2 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi-5 / References: UniProt: Q9JHF9 |
-Sugars , 4 types, 13 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 154 molecules
#7: Water | ChemComp-HOH / |
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-Details
Nonpolymer details | ALL POLYSACCHA |
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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: 3.21 Å3/Da / Density % sol: 61.64 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 6.5 Details: 0.1M Na-Cacodylate, 23% PEG 8000, pH 6.5, VAPOR DIFFUSION, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2007 / Details: mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 23932 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.095 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z63 Resolution: 2.84→20 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.877 / SU B: 36.744 / SU ML: 0.355 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: CYS388 AND CYS389 FORMS AN UNUSUAL DISULFIDE BRIDGE AND A DISTORTED CIS PEPTIDE BOND
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2.84→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.835→2.907 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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