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Yorodumi- PDB-2z65: Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z65 | |||||||||
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Title | Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / TLR4 / toll-like receptor / MD-2 / LPS / E5564 / eritoran / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Leucine-rich repeat / Membrane / Transmembrane / Secreted | |||||||||
Function / homology | Function and homology information nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / detection of fungus / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / lipopolysaccharide immune receptor activity / Toll-like receptor 4 binding / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / detection of lipopolysaccharide ...nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / detection of fungus / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / lipopolysaccharide immune receptor activity / Toll-like receptor 4 binding / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / detection of lipopolysaccharide / regulation of dendritic cell cytokine production / intestinal epithelial structure maintenance / MyD88-independent TLR4 cascade / TRIF-mediated programmed cell death / negative regulation of interleukin-23 production / I-kappaB phosphorylation / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / Caspase activation via Death Receptors in the presence of ligand / wound healing involved in inflammatory response / B cell proliferation involved in immune response / Toll Like Receptor 4 (TLR4) Cascade / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of interleukin-1 production / positive regulation of lipopolysaccharide-mediated signaling pathway / macrophage activation / Regulation of TLR by endogenous ligand / microglia differentiation / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / positive regulation of macrophage activation / 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 / MyD88 deficiency (TLR2/4) / 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 / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / phagocytic cup / T-helper 1 type immune response / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / negative regulation of osteoclast differentiation / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of interferon-alpha production / 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 / cellular defense response / coreceptor activity / phagocytosis / positive regulation of B cell proliferation / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / ERK1 and ERK2 cascade / ruffle / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / nitric oxide biosynthetic process / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / 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 / Heme signaling / positive regulation of MAP kinase activity / negative regulation of ERK1 and ERK2 cascade / 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 / cellular response to mechanical stimulus / cellular response to amyloid-beta / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / signaling receptor activity / gene expression / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Eptatretus burgeri (inshore hagfish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 2z65.cif.gz | 191.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z65.ent.gz | 150.9 KB | Display | PDB format |
PDBx/mmJSON format | 2z65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z65 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z65 | HTTPS FTP |
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-Related structure data
Related structure data | 2z62SC 2z63C 2z64SC 2z66C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
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Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 31141.719 Da / Num. of mol.: 2 Fragment: TV3, UNP residues 27-228(human), E5564, UNP residues 19-158(Inshore hagfish) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus burgeri (inshore hagfish) Gene: TLR4, VLRB.61 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi-5 / References: UniProt: O00206, UniProt: Q4G1L2 #2: Protein | Mass: 16184.761 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MD-2 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi-5 / References: UniProt: Q9Y6Y9 |
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-Sugars , 2 types, 6 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-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: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 165 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | POLYSACCHARIDES WERE ORIGINALLY ASSIGNED TO CHAINS M1401, M(1301-1304), M1201, N1401, N1301, AND ...POLYSACCHA |
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Sequence details | THIS CONSTRUCT INCLUDES A LINKER THAT CONSIST OF 229TH LYS AND 230TH GLU. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.24 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 4.5 Details: 0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K |
-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: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 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: 2.7→50 Å / Num. all: 30860 / Num. obs: 27898 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.089 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z62, 2Z64 Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.864 / SU B: 33.68 / SU ML: 0.35 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 50.542 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.7→2.769 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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