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- PDB-1fyw: CRYSTAL STRUCTURE OF THE TIR DOMAIN OF HUMAN TLR2 -

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Basic information

Entry
Database: PDB / ID: 1fyw
TitleCRYSTAL STRUCTURE OF THE TIR DOMAIN OF HUMAN TLR2
ComponentsTOLL-LIKE RECEPTOR 2
KeywordsSIGNALING PROTEIN / beta-alpha-beta fold parallel beta sheet / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / toll-like receptor TLR6:TLR2 signaling pathway / 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 ...Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / toll-like receptor TLR6:TLR2 signaling pathway / 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 / negative regulation of synapse assembly / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / lipopolysaccharide immune receptor activity / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / toll-like receptor 2 signaling pathway / positive regulation of matrix metallopeptidase secretion / I-kappaB phosphorylation / nitric oxide metabolic process / central nervous system myelin formation / Toll-like receptor binding / positive regulation of interleukin-18 production / leukotriene metabolic process / Regulation of TLR by endogenous ligand / response to fatty acid / peptidoglycan binding / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / microglia development / MyD88 deficiency (TLR2/4) / negative regulation of phagocytosis / pattern recognition receptor activity / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor signaling pathway / positive regulation of oligodendrocyte differentiation / positive regulation of nitric-oxide synthase biosynthetic process / cellular response to lipoteichoic acid / positive regulation of interleukin-10 production / positive regulation of Wnt signaling pathway / positive regulation of chemokine production / positive regulation of interferon-beta production / positive regulation of interleukin-12 production / secretory granule membrane / response to progesterone / learning / cell projection / positive regulation of interleukin-8 production / lipopolysaccharide binding / microglial cell activation / response to insulin / response to toxic substance / 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 / phagocytic vesicle membrane / Modulation by Mtb of host immune system / transmembrane signaling receptor activity / positive regulation of tumor necrosis factor production / signaling receptor activity / cell body / amyloid-beta binding / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / defense response to virus / response to hypoxia / receptor complex / defense response to Gram-positive bacterium / immune response / inflammatory response / membrane raft / negative regulation of cell population proliferation / innate immune response / apoptotic process / Neutrophil degranulation / protein-containing complex binding / positive regulation of gene expression / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. ...Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsXu, Y. / Tao, X. / Shen, B. / Horng, T. / Medzhitov, R. / Manley, J.L. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nature / Year: 2000
Title: Structural basis for signal transduction by the Toll/interleukin-1 receptor domains.
Authors: Xu, Y. / Tao, X. / Shen, B. / Horng, T. / Medzhitov, R. / Manley, J.L. / Tong, L.
History
DepositionOct 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TOLL-LIKE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)18,4551
Polymers18,4551
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TOLL-LIKE RECEPTOR 2

A: TOLL-LIKE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)36,9102
Polymers36,9102
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_675-x+1,-y+2,z1
Buried area2190 Å2
ΔGint-21 kcal/mol
Surface area17130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.2, 121.2, 91.6
Angle α, β, γ (deg.)90, 90, 120
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein TOLL-LIKE RECEPTOR 2 /


Mass: 18455.197 Da / Num. of mol.: 1 / Fragment: TIR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O60603

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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: 5.26 Å3/Da / Density % sol: 76.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM cacodylate, 10 % PEG 8000, 20 % DMSO, 200 mM MgCl2, 5 mM DTT, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMcacodylate1reservoir
210 %PEG80001reservoir
320 %(v/v)DMSO1reservoir
4200 mM1reservoirMgCl2
55 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 7500 / Num. obs: 7380 / % possible obs: 99 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 32
Reflection shellResolution: 3→3.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.239 / % possible all: 97

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Processing

Software
NameVersionClassification
COMO+ MADSYSphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MADSYSphasing
RefinementResolution: 3→20 Å / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.274 550 7.5%
Rwork0.244 --
all0.26 7500 -
obs0.244 7451 -
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 0 0 1266
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 7.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

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