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Yorodumi- PDB-3fxi: Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fxi | |||||||||
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Title | Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Leucine Rich Repeat / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Membrane / Receptor / 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 / regulation of dendritic cell cytokine production ...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 / regulation of dendritic cell cytokine production / detection of lipopolysaccharide / intestinal epithelial structure maintenance / MyD88-independent TLR4 cascade / TRIF-mediated programmed cell death / I-kappaB phosphorylation / negative regulation of interleukin-23 production / 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 / Caspase activation via Death Receptors in the presence of ligand / B cell proliferation involved in immune response / nucleotide-binding oligomerization domain containing 1 signaling pathway / Toll Like Receptor 4 (TLR4) Cascade / positive regulation of interleukin-1 production / positive regulation of stress-activated MAPK cascade / positive regulation of lipopolysaccharide-mediated signaling pathway / macrophage activation / Regulation of TLR by endogenous ligand / astrocyte development / TRIF-dependent toll-like receptor signaling pathway / microglia differentiation / nucleotide-binding oligomerization domain containing 2 signaling pathway / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of interleukin-17 production / positive regulation of MHC class II biosynthetic process / positive regulation of platelet activation / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage activation / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 2 production / MyD88 deficiency (TLR2/4) / 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 / positive regulation of NLRP3 inflammasome complex assembly / T-helper 1 type immune response / toll-like receptor signaling pathway / RSV-host interactions / 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 / cellular response to lipoteichoic acid / phagocytic cup / positive regulation of interleukin-10 production / negative regulation of interleukin-6 production / Respiratory syncytial virus (RSV) attachment and entry / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / positive regulation of interferon-alpha production / cellular defense response / coreceptor activity / phagocytosis / stress-activated MAPK cascade / positive regulation of chemokine production / positive regulation of B cell proliferation / JNK cascade / lipopolysaccharide-mediated signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / ruffle / nitric oxide biosynthetic process / TRAF6-mediated induction of TAK1 complex within TLR4 complex / ERK1 and ERK2 cascade / 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 / positive regulation of MAP kinase activity / Heme signaling / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / cellular response to amyloid-beta / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / signaling receptor activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Park, B.S. / Song, D.H. / Kim, H.M. / Lee, J.-O. | |||||||||
Citation | Journal: Nature / Year: 2009 Title: The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex Authors: Park, B.S. / Song, D.H. / Kim, H.M. / Choi, B.-S. / Lee, H. / 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 | 3fxi.cif.gz | 322.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fxi.ent.gz | 257.2 KB | Display | PDB format |
PDBx/mmJSON format | 3fxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fxi_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 3fxi_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 3fxi_validation.xml.gz | 60.5 KB | Display | |
Data in CIF | 3fxi_validation.cif.gz | 79.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/3fxi ftp://data.pdbj.org/pub/pdb/validation_reports/fx/3fxi | HTTPS FTP |
-Related 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: 68838.328 Da / Num. of mol.: 2 / Fragment: extracellular domain, residues 27-631 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TLR4 / Plasmid: pAcGP67A / Cell (production host): HIGH FIVE CELLS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O00206 #2: Protein | Mass: 16385.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESOP1, LY96, MD-2, MD2 / Plasmid: pAcGP67A / Cell (production host): HIGH FIVE CELLS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y6Y9 |
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-Sugars , 4 types, 14 molecules
#3: Polysaccharide | L-glycero-alpha-D-manno-heptopyranose-(1-7)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero- ...L-glycero-alpha-D-manno-heptopyranose-(1-7)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-alpha-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#4: 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 #5: Polysaccharide | L-glycero-alpha-D-manno-heptopyranose-(1-7)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero- ...L-glycero-alpha-D-manno-heptopyranose-(1-7)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #10: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 24 molecules
#6: Chemical | ChemComp-FTT / #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-PO4 / #11: Chemical | #12: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | RESIDUES FROM 1001 TO 1018 IN THE CHAINS A AND B ARE E.COLI LIPOPOLYSA |
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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: 3.51 Å3/Da / Density % sol: 64.91 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50mM MgCl2, 0.1M Na-HEPES pH 7.5, 30% PEG MME 550, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 24, 2008 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→47.87 Å / Num. all: 44174 / Num. obs: 41586 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 91.7 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 13.59 |
Reflection shell | Resolution: 3.1→3.4 Å / Redundancy: 5 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.88 / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z65, 2Z66 Resolution: 3.1→47.87 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2098397.3 / Data cutoff low absF: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 174.67 Å2 / Biso mean: 82.2 Å2 / Biso min: 35.78 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→47.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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