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Open data
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Basic information
Entry | Database: PDB / ID: 3a79 | |||||||||
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Title | Crystal structure of TLR2-TLR6-Pam2CSK4 complex | |||||||||
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![]() | IMMUNE SYSTEM / Toll-like Receptor / diacyl lipopeptide / innate immunity / Leucine Rich Repeat / Cell membrane / Cytoplasmic vesicle / Disulfide bond / Glycoprotein / Immune response / Inflammatory response / LEUCINE-RICH REPEAT / Membrane / Receptor / Transmembrane / Phosphoprotein | |||||||||
Function / homology | ![]() toll-like receptor 6 signaling pathway / negative regulation of tumor necrosis factor production => GO:0032720 / interleukin-1 beta production / : / response to bacterial lipoprotein / diacyl lipopeptide binding / Beta defensins / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide ...toll-like receptor 6 signaling pathway / negative regulation of tumor necrosis factor production => GO:0032720 / interleukin-1 beta production / : / response to bacterial lipoprotein / diacyl lipopeptide binding / Beta defensins / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / positive regulation of neutrophil migration / cellular response to diacyl bacterial lipopeptide / Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / cellular response to bacterial lipopeptide / Regulation of TLR by endogenous ligand / lipoteichoic acid binding / negative regulation of synapse assembly / response to molecule of fungal origin / negative regulation of toll-like receptor 2 signaling pathway / cell surface pattern recognition receptor signaling pathway / regulation of dendritic cell cytokine production / response to peptidoglycan / Toll-like receptor 2 binding / cellular response to oxidised low-density lipoprotein particle stimulus / NADP+ nucleosidase activity / positive regulation of interleukin-18 production / central nervous system myelin formation / positive regulation of xenophagy / xenophagy / leukotriene metabolic process / neutrophil migration / negative regulation of actin filament polymerization / negative regulation of interleukin-8 production / cell activation / TRIF-dependent toll-like receptor signaling pathway / lipopeptide binding / response to fatty acid / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / cellular response to peptidoglycan / negative regulation of interleukin-12 production / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of cytokine production involved in inflammatory response / negative regulation of interleukin-17 production / positive regulation of macrophage activation / microglia development / positive regulation of macrophage cytokine production / negative regulation of phagocytosis / positive regulation of leukocyte migration / positive regulation of intracellular signal transduction / MyD88-dependent toll-like receptor signaling pathway / pattern recognition receptor activity / positive regulation of reactive oxygen species biosynthetic process / positive regulation of NLRP3 inflammasome complex assembly / toll-like receptor signaling pathway / nitric oxide metabolic process / positive regulation of oligodendrocyte differentiation / leukocyte migration / positive regulation of nitric-oxide synthase biosynthetic process / plasma membrane => GO:0005886 / cellular response to lipoteichoic acid / positive regulation of interleukin-10 production / regulation of presynapse assembly / positive regulation of chemokine production / positive regulation of JUN kinase activity / nitric oxide biosynthetic process / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / Neutrophil degranulation / axonogenesis / positive regulation of interleukin-1 beta production / learning / positive regulation of cytokine production / cell projection / response to bacterium / microglial cell activation / defense response / positive regulation of inflammatory response / positive regulation of interleukin-6 production / cellular response to amyloid-beta / phagocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / cell body / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / defense response to Gram-positive bacterium / inflammatory response / protein heterodimerization activity / membrane raft / negative regulation of cell population proliferation / external side of plasma membrane / innate immune response Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kang, J.Y. / Jin, M.S. / Lee, J.-O. | |||||||||
![]() | ![]() Title: Recognition of lipopeptide patterns by Toll-like receptor 2-Toll-like receptor 6 heterodimer Authors: Kang, J.Y. / Nan, X. / Jin, M.S. / Youn, S.-J. / Ryu, Y.H. / Mah, S. / Han, S.H. / Lee, H. / Paik, S.-G. / Lee, J.-O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 457.9 KB | Display | ![]() |
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PDB format | ![]() | 378.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3a7bC ![]() 3a7cC ![]() 2o6rS ![]() 2z7xS ![]() 2z81S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Toll-like receptor ... , 2 types, 2 molecules AB
#1: Protein | Mass: 65535.309 Da / Num. of mol.: 1 Fragment: extracellular domain, UNP residues 1-506(mouse), UNP residues 133-200(Inshore hagfish) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: Tlr2 / Plasmid: PVL1393 / Production host: ![]() |
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#2: Protein | Mass: 63785.551 Da / Num. of mol.: 1 Fragment: extracellular domain, UNP residues 1-482(mouse), UNP residues 157-232(Inshore hagfish) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: Tlr6 / Plasmid: PVL1393 / Production host: ![]() |
-Protein/peptide / Non-polymers , 2 types, 2 molecules C![](data/chem/img/PXS.gif)
![](data/chem/img/PXS.gif)
#3: Protein/peptide | Mass: 724.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others) |
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#7: Chemical | ChemComp-PXS / ( |
-Sugars , 3 types, 11 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2.0M ammonium sulfate, 0.1M MES pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2008 |
Radiation | Monochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 43746 / Num. obs: 43573 / % possible obs: 99.67 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 56.99 Å2 / Rsym value: 0.106 / Net I/σ(I): 8.27 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.55 % / Mean I/σ(I) obs: 2.33 / Num. unique all: 3448 / Rsym value: 0.525 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 2Z81, 2Z7X, 2O6R Resolution: 2.9→34.11 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.799 / SU ML: 2.75 / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.282 Å2 / ksol: 0.278 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 445.89 Å2 / Biso mean: 88.661 Å2 / Biso min: 24.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→34.11 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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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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