+
Open data
-
Basic information
Entry | Database: PDB / ID: 3ul7 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the TV3 mutant F63W | ||||||||||||
![]() | Toll-like receptor 4, Variable lymphocyte receptor B | ||||||||||||
![]() | IMMUNE SYSTEM / LRR / protein binding / MD-2 / extracellular matrix | ||||||||||||
Function / homology | ![]() 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 / regulation of dendritic cell cytokine production / 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 / 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 / macrophage activation / Regulation of TLR by endogenous ligand / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / microglia differentiation / nucleotide-binding oligomerization domain containing 2 signaling pathway / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of MHC class II biosynthetic process / negative regulation of interleukin-17 production / positive regulation of platelet activation / positive regulation of cytokine production involved in inflammatory response / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of macrophage activation / positive regulation of chemokine (C-X-C motif) ligand 2 production / MyD88 deficiency (TLR2/4) / positive regulation of macrophage cytokine production / negative regulation of cold-induced thermogenesis / 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 / negative regulation of interleukin-6 production / Respiratory syncytial virus (RSV) attachment and entry / phagocytic cup / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / positive regulation of interferon-alpha production / phagocytosis / stress-activated MAPK cascade / positive regulation of chemokine production / positive regulation of B cell proliferation / JNK cascade / lipopolysaccharide-mediated signaling pathway / ruffle / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / nitric oxide biosynthetic process / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / TRAF6-mediated induction of TAK1 complex within TLR4 complex / 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 / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / gene expression / ER-Phagosome pathway Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kim, H.J. / Cheong, H.K. / Jeon, Y.H. | ||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 73.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 778.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 783.7 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ul8C ![]() 3ul9C ![]() 3ulaC ![]() 2z62S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() Gene: TLR4, VLRB / Production host: ![]() ![]() |
---|
-Sugars , 3 types, 3 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/FUL.gif)
![](data/chem/img/FUL.gif)
#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 |
---|---|
#3: Sugar | ChemComp-NAG / |
#4: Sugar | ChemComp-FUL / |
-Non-polymers , 2 types, 53 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | THE FUSION PROTEIN OF TLR4 (UNP RESIDUES 28-228) AND VLRB.61 (UNP RESIDUES 126-199) |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.81 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() |
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 |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2Z62 Resolution: 2.37→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: maximum likelihood
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.37→50 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.37→2.45 Å |