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- PDB-1o77: CRYSTAL STRUCTURE OF THE C713S MUTANT OF THE TIR DOMAIN OF HUMAN TLR2 -

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Basic information

Entry
Database: PDB / ID: 1o77
TitleCRYSTAL STRUCTURE OF THE C713S MUTANT OF THE TIR DOMAIN OF HUMAN TLR2
ComponentsTOLL-LIKE RECEPTOR 2
KeywordsIMMUNE SYSTEM/MEMBRANE PROTEIN / KNOWN BIOLOGICAL ACTIVITY RECEPTOR / IMMUNE RESPONSE / INFLAMMATORY RESPONSE / TRANSMEMBRANE / LEUCINE-RICH REPEAT / GLYCOPROTEIN / 3D-STRUCTURE. / IMMUNE SYSTEM-MEMBRANE PROTEIN complex
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 / 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 ...Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / 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 / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / lipopolysaccharide immune receptor activity / toll-like receptor 2 signaling pathway / positive regulation of matrix metallopeptidase secretion / Toll-like receptor binding / positive regulation of interleukin-18 production / toll-like receptor TLR6:TLR2 signaling pathway / Regulation of TLR by endogenous ligand / peptidoglycan binding / NAD+ nucleosidase activity, cyclic ADP-ribose generating / microglia development / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor signaling pathway / negative regulation of phagocytosis / pattern recognition receptor activity / RSV-host interactions / cellular response to lipoteichoic acid / positive regulation of Wnt signaling pathway / positive regulation of chemokine production / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / secretory granule membrane / positive regulation of interleukin-8 production / learning / lipopolysaccharide binding / : / cellular response to type II interferon / positive regulation of interleukin-6 production / phagocytic vesicle membrane / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / Modulation by Mtb of host immune system / transmembrane signaling receptor activity / signaling receptor activity / amyloid-beta binding / ER-Phagosome pathway / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / receptor complex / defense response to Gram-positive bacterium / immune response / membrane raft / inflammatory response / innate immune response / intracellular membrane-bounded organelle / apoptotic process / Neutrophil degranulation / positive regulation of gene expression / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeats, bacterial type / TIR domain profile. ...Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeats, bacterial type / 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 / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTao, X. / Xu, Y. / Ye, Z. / Beg, A.A. / Tong, L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: An Extensively Associated Dimer in the Structure of the C713S Mutant of the Tir Domain of Human Tlr2
Authors: Tao, X. / Xu, Y. / Zheng, Y. / Beg, A.A. / Tong, L.
History
DepositionOct 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TOLL-LIKE RECEPTOR 2
B: TOLL-LIKE RECEPTOR 2
C: TOLL-LIKE RECEPTOR 2
D: TOLL-LIKE RECEPTOR 2
E: TOLL-LIKE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)87,6215
Polymers87,6215
Non-polymers00
Water00
1
A: TOLL-LIKE RECEPTOR 2
B: TOLL-LIKE RECEPTOR 2
C: TOLL-LIKE RECEPTOR 2
D: TOLL-LIKE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)70,0974
Polymers70,0974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-25.28 kcal/mol
Surface area29180 Å2
MethodPISA
2
E: TOLL-LIKE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)17,5241
Polymers17,5241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)112.300, 112.300, 362.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsCHAINS A,B,C AND D FORM A TETRAMER- LIKE ASSOCIATIONIN THE ASYMMETRIC UNIT

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Components

#1: Protein
TOLL-LIKE RECEPTOR 2 / TOLL/INTERLEUKIN 1 RECEPTOR-LIKE PROTEIN 4 / TLR2 / TIL4


Mass: 17524.141 Da / Num. of mol.: 5 / Fragment: TIR DOMAIN, RESIDUES 639-784 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60603
Compound detailsENGINEERED MUTATION CYS 713 SER IN CHAINS A, B, C D AND E MEDIATES THE INNATE IMMUNE RESPONSE TO ...ENGINEERED MUTATION CYS 713 SER IN CHAINS A, B, C D AND E MEDIATES THE INNATE IMMUNE RESPONSE TO BACTERIAL LIPOPROTEINS AND OTHER MICROBIAL CELL WALL COMPONENTS LEADING TO THE ACTIVATION OF NF-KAPPA-B, SECRETION OF CYTOKINES AND AN INFLAMMATORY RESPONSE. HIGH LEVEL OF EXPRESSION IN PERIPHERAL BLOOD LEUKOCYTES (MONOCYTES), BONE MARROW AND SPLEEN. SIMILAR TO THE TOLL FAMILY OF RECEPTORS.
Has protein modificationY

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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: 3.48 Å3/Da / Density % sol: 64.33 %
Crystal growpH: 7 / Details: 1.4M (NH4)2HPO4, 0.1M MES PH 6.5
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMMES1reservoirpH6.5, or HEPES(pH7.5)
21.2-1.4 M1reservoir(NH4)2HPO4
35 mMdithiothreitol1reservoir
410-20 mg/mlprotein1drop
520 mMMOPS1droppH7.0
6150 mM1dropNaCl
72 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9876
DetectorDate: Jun 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9876 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 23135 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 15
Reflection shellResolution: 3.31→3.4 Å / Redundancy: 3 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 10 / % possible all: 99.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 99505

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FYW

1fyw


Resolution: 3.2→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.315 1453 7.4 %RANDOM
Rwork0.249 ---
obs0.249 19713 84.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.3326 Å2 / ksol: 0.284113 e/Å3
Displacement parametersBiso mean: 71.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.12 Å2-7.86 Å20 Å2
2--13.77 Å20 Å2
3----9.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5824 0 0 0 5824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 166 7.5 %
Rwork0.28 2045 -
obs--58.6 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.316
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
LS refinement shell
*PLUS
Rfactor Rfree: 0.368 / Rfactor Rwork: 0.308

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