+Open data
-Basic information
Entry | Database: PDB / ID: 3ul7 | ||||||||||||
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Title | Crystal structure of the TV3 mutant F63W | ||||||||||||
Components | Toll-like receptor 4, Variable lymphocyte receptor B | ||||||||||||
Keywords | IMMUNE SYSTEM / LRR / protein binding / MD-2 / extracellular matrix | ||||||||||||
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 / 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 ...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 / 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 / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to oxidised low-density lipoprotein particle stimulus / Toll Like Receptor 4 (TLR4) Cascade / Caspase activation via Death Receptors in the presence of ligand / wound healing involved in inflammatory response / B cell proliferation involved in immune response / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of interleukin-1 production / 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 / NADP+ nucleosidase activity / positive regulation of platelet activation / positive regulation of cytokine production involved in inflammatory response / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of MHC class II biosynthetic process / 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 / IRAK4 deficiency (TLR2/4) / positive regulation of reactive oxygen species biosynthetic process / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / phagocytic cup / positive regulation of NLRP3 inflammasome complex assembly / toll-like receptor signaling pathway / 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 / phagocytosis / positive regulation of B cell proliferation / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / ruffle / ERK1 and ERK2 cascade / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / nitric oxide biosynthetic process / positive regulation of interferon-beta production / positive regulation of interleukin-12 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 / amyloid-beta binding / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Eptatretus burgeri (inshore hagfish) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å | ||||||||||||
Authors | Kim, H.J. / Cheong, H.K. / Jeon, Y.H. | ||||||||||||
Citation | Journal: Plos One / Year: 2012 Title: Structure-Based Rational Design of a Toll-like Receptor 4 (TLR4) Decoy Receptor with High Binding Affinity for a Target Protein. Authors: Han, J. / Kim, H.J. / Lee, S.C. / Hong, S. / Park, K. / Jeon, Y.H. / Kim, D. / Cheong, H.K. / Kim, H.S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ul7.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ul7.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ul7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/3ul7 ftp://data.pdbj.org/pub/pdb/validation_reports/ul/3ul7 | HTTPS FTP |
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-Related structure data
Related structure data | 3ul8C 3ul9C 3ulaC 2z62S 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 , 1 types, 1 molecules A
#1: Protein | Mass: 31296.875 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 28-228, UNP RESIDUES 126-199 / Mutation: F63W Source method: isolated from a genetically manipulated source Details: THE FUSION PROTEIN OF TLR4 (UNP RESIDUES 28-228) AND VLRB (UNP RESIDUES 126-199) Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus burgeri (inshore hagfish) Gene: TLR4, VLRB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O00206, UniProt: Q4G1L2 |
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-Sugars , 3 types, 3 molecules
#2: 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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#3: Sugar | ChemComp-NAG / |
#4: Sugar | ChemComp-FUL / |
-Non-polymers , 2 types, 53 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE FUSION PROTEIN OF TLR4 (UNP RESIDUES 28-228) AND VLRB.61 (UNP RESIDUES 126-199) |
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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: 2.55 Å3/Da / Density % sol: 51.81 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 5.5 Details: 0.1M Bis-Tris (pH5.5), 36% PEG 1000, 0.2M Lithium sulfate, VAPOR DIFFUSION, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2010 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→50 Å / Num. obs: 13192 / % possible obs: 96.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.37→2.45 Å / % possible all: 76.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Z62 Resolution: 2.37→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: maximum likelihood
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Refinement step | Cycle: LAST / Resolution: 2.37→50 Å
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LS refinement shell | Resolution: 2.37→2.45 Å |