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- PDB-8ar0: Solution structure of TLR2 transmembrane and cytoplasmic juxtamem... -

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Basic information

Entry
Database: PDB / ID: 8ar0
TitleSolution structure of TLR2 transmembrane and cytoplasmic juxtamembrane regions
ComponentsToll-like receptor 2
KeywordsMEMBRANE PROTEIN / PROTEIN
Function / homology
Function and homology information


toll-like receptor TLR6:TLR2 signaling pathway / 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 ...toll-like receptor TLR6:TLR2 signaling pathway / 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 / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / negative regulation of synapse assembly / 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 / positive regulation of interleukin-18 production / Toll-like receptor binding / central nervous system myelin formation / leukotriene metabolic process / Regulation of TLR by endogenous ligand / response to fatty acid / peptidoglycan binding / NAD+ nucleotidase, cyclic ADP-ribose generating / 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 / nitric oxide metabolic process / RSV-host interactions / 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 interleukin-12 production / positive regulation of interferon-beta production / secretory granule membrane / learning / cell projection / positive regulation of interleukin-8 production / response to progesterone / lipopolysaccharide binding / microglial cell activation / response to insulin / response to toxic substance / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / phagocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / Modulation by Mtb of host immune system / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / ER-Phagosome pathway / cell body / defense response to virus / receptor complex / response to hypoxia / defense response to Gram-positive bacterium / inflammatory response / immune 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-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 ...Leucine rich repeat C-terminal 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
Similarity search - Domain/homology
Toll-like receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKornilov, F.D. / Shabalkina, A.V. / Goncharuk, M.V. / Goncharuk, S.A. / Arseniev, A.S. / Mineev, K.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation22-14-0020 Russian Federation
CitationJournal: Nat Commun / Year: 2023
Title: The architecture of transmembrane and cytoplasmic juxtamembrane regions of Toll-like receptors.
Authors: Kornilov, F.D. / Shabalkina, A.V. / Lin, C. / Volynsky, P.E. / Kot, E.F. / Kayushin, A.L. / Lushpa, V.A. / Goncharuk, M.V. / Arseniev, A.S. / Goncharuk, S.A. / Wang, X. / Mineev, K.S.
History
DepositionAug 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)5,8521
Polymers5,8521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, no extra NOE peaks, NMR relaxation study, values of tau c of alpha helix residues conform to monomer assembly
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Toll-like receptor 2 / Toll/interleukin-1 receptor-like protein 4


Mass: 5852.218 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR2, TIL4 / Production host: Escherichia coli (E. coli) / References: UniProt: O60603

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
152isotropic12D 1H-13C HSQC aliphatic
172isotropic12D 1H-13C HSQC aliphatic constant time
162isotropic12D 1H-13C HSQC aromatic
132isotropic13D HNCO
142isotropic13D HN(CO)CA
122isotropic13D HNCA
182isotropic13D (H)CCH-TOCSY
192isotropic13D (H)CCH-TOCSY
1172isotropic13D (H)CCH-TOCSY constant time
1162isotropic13D (H)CCH-TOCSY constant time
1102isotropic13D 1H-15N NOESY
1112isotropic13D 1H-13C NOESY aliphatic
1142isotropic13D 1H-13C NOESY aliphatic constant time
1122isotropic13D (H)CCH-COSY aromatic
1132isotropic12D CBHD aromatic
2183anisotropic12D 1H-15N IPAP-HSQC
2193anisotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
bicelle2200 uM [U-13C; U-15N] protein, 23.27 mM DMPC, 5.87 mM DMPG, 78.16 mM DHPC, 20 mM potassium phosphate, 4 mM TCEP, 0.05 % w/v sodium azide, 1 mM TSP, 95% H2O/5% D2O15N13C_sample95% H2O/5% D2O
bicelle3188 uM [U-15N] protein, 24.23 mM DMPC, 5.50 mM DMPG, 80.18 mM DHPC, 50 mM potassium phosphate, 4 mM TCEP, 0.05 % w/v sodium azide, 1 mM TSP, 30 mg/mL dGpG, 100 mM potassium chloride, 95% H2O/5% D2O15N_sample_forRDC95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMprotein[U-13C; U-15N]2
23.27 mMDMPCnatural abundance2
5.87 mMDMPGnatural abundance2
78.16 mMDHPCnatural abundance2
20 mMpotassium phosphatenatural abundance2
4 mMTCEPnatural abundance2
0.05 % w/vsodium azidenatural abundance2
1 mMTSPnatural abundance2
188 uMprotein[U-15N]3
24.23 mMDMPCnatural abundance3
5.50 mMDMPGnatural abundance3
80.18 mMDHPCnatural abundance3
50 mMpotassium phosphatenatural abundance3
4 mMTCEPnatural abundance3
0.05 % w/vsodium azidenatural abundance3
1 mMTSPnatural abundance3
30 mg/mLdGpGnatural abundance3
100 mMpotassium chloridenatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPH errPressure (kPa)Temperature (K)
150 mMconditions_main7.0 0.1AMBIENT atm318 K
2235 mMconditions_RDC7.0 0.1AMBIENT atm318 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Peter Guentertstructure calculation
TopSpin3Bruker Biospinprocessing
CARA1.9.7.1Keller and Wuthrichchemical shift assignment
CARA1.9.7.1Keller and Wuthrichpeak picking
qMDD3.2Maxim Mayzel, Krzysztof Kazimierczuk, Vladislav Orekhovprocessing
MOLMOLKoradi, Billeter and Wuthrichdata analysis
PyMOLSchrodinger, Inc.data analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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