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- PDB-4om7: Crystal structure of TIR domain of TLR6 -

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Basic information

Entry
Database: PDB / ID: 4om7
TitleCrystal structure of TIR domain of TLR6
ComponentsToll-like receptor 6
KeywordsSIGNALING PROTEIN / TIR fold / Protein interaction
Function / homology
Function and homology information


toll-like receptor 6 signaling pathway / regulation of cytokine production => GO:0001817 / interleukin-1 beta production / : / toll-like receptor TLR6:TLR2 signaling pathway / Toll Like Receptor TLR6:TLR2 Cascade / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / cellular response to diacyl bacterial lipopeptide / cellular response to bacterial lipopeptide ...toll-like receptor 6 signaling pathway / regulation of cytokine production => GO:0001817 / interleukin-1 beta production / : / toll-like receptor TLR6:TLR2 signaling pathway / Toll Like Receptor TLR6:TLR2 Cascade / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / cellular response to diacyl bacterial lipopeptide / cellular response to bacterial lipopeptide / negative regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / NADP+ nucleosidase activity / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of interleukin-8 production / Regulation of TLR by endogenous ligand / cell activation / lipopeptide binding / TRIF-dependent toll-like receptor signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / activation of NF-kappaB-inducing kinase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage activation / MyD88 deficiency (TLR2/4) / 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 / positive regulation of NLRP3 inflammasome complex assembly / toll-like receptor signaling pathway / nitric oxide metabolic process / plasma membrane => GO:0005886 / positive regulation of JUN kinase activity / microglial cell activation / cellular response to amyloid-beta / phagocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / positive regulation of nitric oxide biosynthetic process / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / ER-Phagosome pathway / positive regulation of canonical NF-kappaB signal transduction / receptor complex / defense response to bacterium / inflammatory response / immune response / membrane raft / protein heterodimerization activity / innate immune response / signaling receptor binding / positive regulation of gene expression / Golgi apparatus / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Toll-like receptor 6 / Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain ...Toll-like receptor 6 / Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Toll-like receptor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsPark, H.H. / Jang, T.H.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Crystal Structure of TIR Domain of TLR6 Reveals Novel Dimeric Interface of TIR-TIR Interaction for Toll-Like Receptor Signaling Pathway.
Authors: Jang, T.H. / Park, H.H.
History
DepositionJan 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toll-like receptor 6
B: Toll-like receptor 6


Theoretical massNumber of molelcules
Total (without water)42,4212
Polymers42,4212
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-11 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.607, 44.199, 75.723
Angle α, β, γ (deg.)90.00, 118.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-910-

HOH

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Components

#1: Protein Toll-like receptor 6


Mass: 21210.295 Da / Num. of mol.: 2 / Fragment: UNP residues 640-796
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2C9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.2M lithium sulfate monohydrate, 0.1M Tris pH 8.6, 25%(w/v) polyethylene glycol 3350 and 4%(v/v) formamide, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 18245 / % possible obs: 14 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4
Reflection shellResolution: 2.2→2.4 Å / % possible all: 92

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.204→31.822 Å / SU ML: 0.32 / σ(F): 0.6 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 944 5.18 %random
Rwork0.2334 ---
obs0.236 18212 96.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.204→31.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 0 27 2431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092483
X-RAY DIFFRACTIONf_angle_d1.393362
X-RAY DIFFRACTIONf_dihedral_angle_d14.909904
X-RAY DIFFRACTIONf_chiral_restr0.092352
X-RAY DIFFRACTIONf_plane_restr0.008424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.204-2.320.35151200.30712461X-RAY DIFFRACTION96
2.32-2.46530.30941350.29492451X-RAY DIFFRACTION97
2.4653-2.65560.31141410.27222471X-RAY DIFFRACTION97
2.6556-2.92260.3261450.26172510X-RAY DIFFRACTION98
2.9226-3.34520.28841500.24992485X-RAY DIFFRACTION98
3.3452-4.2130.2641400.21342482X-RAY DIFFRACTION96
4.213-31.82550.27481130.21422408X-RAY DIFFRACTION90

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