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- PDB-8ar3: Solution structure of TLR9 transmembrane and cytoplasmic juxtamem... -

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Basic information

Entry
Database: PDB / ID: 8ar3
TitleSolution structure of TLR9 transmembrane and cytoplasmic juxtamembrane regions
ComponentsToll-like receptor 9
KeywordsMEMBRANE PROTEIN / PROTEIN
Function / homology
Function and homology information


positive regulation of toll-like receptor signaling pathway / regulation of toll-like receptor 9 signaling pathway / cellular response to chloroquine / negative regulation of ATPase-coupled calcium transmembrane transporter activity / Toll Like Receptor 9 (TLR9) Cascade / regulation of B cell differentiation / endolysosome / cellular response to metal ion / regulation of dendritic cell cytokine production / positive regulation of toll-like receptor 9 signaling pathway ...positive regulation of toll-like receptor signaling pathway / regulation of toll-like receptor 9 signaling pathway / cellular response to chloroquine / negative regulation of ATPase-coupled calcium transmembrane transporter activity / Toll Like Receptor 9 (TLR9) Cascade / regulation of B cell differentiation / endolysosome / cellular response to metal ion / regulation of dendritic cell cytokine production / positive regulation of toll-like receptor 9 signaling pathway / I-kappaB phosphorylation / maintenance of gastrointestinal epithelium / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / negative regulation of toll-like receptor signaling pathway / positive regulation of interleukin-18 production / positive regulation of B cell activation / negative regulation of interleukin-8 production / unmethylated CpG binding / siRNA binding / early phagosome / endolysosome membrane / interleukin-1 receptor binding / Trafficking and processing of endosomal TLR / positive regulation of granulocyte macrophage colony-stimulating factor production / MyD88-dependent toll-like receptor signaling pathway / pattern recognition receptor activity / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / positive regulation of nitric-oxide synthase biosynthetic process / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / PI3K Cascade / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction / positive regulation of autophagy / positive regulation of B cell proliferation / positive regulation of chemokine production / positive regulation of JUN kinase activity / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / microglial cell activation / response to molecule of bacterial origin / negative regulation of ERK1 and ERK2 cascade / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / male gonad development / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / positive regulation of NF-kappaB transcription factor activity / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / Potential therapeutics for SARS / positive regulation of MAPK cascade / lysosome / endosome membrane / endosome / defense response to bacterium / apical plasma membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / positive regulation of gene expression / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Leucine-rich repeat unit / Leucine-rich repeat / Leucine Rich repeat / TIR domain / Leucine-rich repeats, bacterial type / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...Leucine-rich repeat unit / Leucine-rich repeat / Leucine Rich repeat / TIR domain / Leucine-rich repeats, bacterial type / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / 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 9
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toll-like receptor 9


Theoretical massNumber of molelcules
Total (without water)5,8061
Polymers5,8061
Non-polymers00
Water0
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)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Toll-like receptor 9 /


Mass: 5805.931 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR9, UNQ5798/PRO19605 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR96

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic constant time
131isotropic12D 1H-13C HSQC aliphatic
141isotropic12D 1H-13C HSQC aromatic
151isotropic13D HNCO
161isotropic13D HNCA
171isotropic13D HN(CO)CA
181isotropic13D (H)CCH-TOCSY
191isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY aliphatic
1111isotropic12D CBHD aromatic
1121isotropic13D (H)CCH-COSY aromatic
2132anisotropic22D 1H-15N HSQC
2142anisotropic22D 1H-15N IPAP-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle11000 uM [U-13C; U-15N] protein, 119 mM LPPC, 41 mM LPPG, 20 mM potassium phosphate, 5 mM TCEP, 1 mM TSP, 95% H2O/5% D2O15N13C_sample95% H2O/5% D2O
micelle2180 uM [U-15N] protein, 84 mM LPPC, 22 mM LPPG, 30 mM potassium phosphate, 5 mM TCEP, 1 mM TSP, 28 mg/mL dGpG, 80 mM potassium chloride, 0.05 % w/v sodium azide, 95% H2O/5% D2O15N_sample_forRDC95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1000 uMprotein[U-13C; U-15N]1
119 mMLPPCnatural abundance1
41 mMLPPGnatural abundance1
20 mMpotassium phosphatenatural abundance1
5 mMTCEPnatural abundance1
1 mMTSPnatural abundance1
180 uMprotein[U-15N]2
84 mMLPPCnatural abundance2
22 mMLPPGnatural abundance2
30 mMpotassium phosphatenatural abundance2
5 mMTCEPnatural abundance2
1 mMTSPnatural abundance2
28 mg/mLdGpGnatural abundance2
80 mMpotassium chloridenatural abundance2
0.05 % w/vsodium azidenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPH errPressure (kPa)Temperature (K)
150 mMconditions_main7.0 0.1AMBIENT atm318 K
2170 mMconditions_RDC7.0 0.1AMBIENT atm318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure 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
PyMOLSchrodinger, Inc.data analysis
MOLMOLKoradi, Billeter and Wuthrichdata 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: 20

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