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- PDB-8ar1: Solution structure of TLR3 transmembrane and cytoplasmic juxtamem... -

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Basic information

Entry
Database: PDB / ID: 8ar1
TitleSolution structure of TLR3 transmembrane and cytoplasmic juxtamembrane regions
ComponentsToll-like receptor 3
KeywordsMEMBRANE PROTEIN / PROTEIN
Function / homology
Function and homology information


TLR3 deficiency - HSE / UNC93B1 deficiency - HSE / TICAM1 deficiency - HSE / type III interferon production / positive regulation of type III interferon production / response to dsRNA / TRAF3 deficiency - HSE / regulation of dendritic cell cytokine production / Toll Like Receptor 3 (TLR3) Cascade / I-kappaB phosphorylation ...TLR3 deficiency - HSE / UNC93B1 deficiency - HSE / TICAM1 deficiency - HSE / type III interferon production / positive regulation of type III interferon production / response to dsRNA / TRAF3 deficiency - HSE / regulation of dendritic cell cytokine production / Toll Like Receptor 3 (TLR3) Cascade / I-kappaB phosphorylation / TLR3-mediated TICAM1-dependent programmed cell death / inflammatory response to wounding / toll-like receptor 3 signaling pathway / necroptotic signaling pathway / detection of virus / activation of NF-kappaB-inducing kinase activity / RIP-mediated NFkB activation via ZBP1 / hyperosmotic response / endolysosome membrane / positive regulation of cytokine production involved in inflammatory response / Trafficking and processing of endosomal TLR / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / RSV-host interactions / cellular response to exogenous dsRNA / response to exogenous dsRNA / negative regulation of osteoclast differentiation / cellular response to interferon-beta / positive regulation of interferon-alpha production / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / JNK cascade / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / TICAM1, RIP1-mediated IKK complex recruitment / extracellular matrix / positive regulation of interleukin-8 production / positive regulation of JNK cascade / microglial cell activation / cellular response to virus / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / transmembrane signaling receptor activity / positive regulation of angiogenesis / male gonad development / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / double-stranded RNA binding / cellular response to xenobiotic stimulus / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / early endosome / endosome membrane / defense response to bacterium / positive regulation of apoptotic process / lysosomal membrane / Golgi membrane / innate immune response / positive regulation of gene expression / endoplasmic reticulum membrane / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / Toll-like receptor / Leucine Rich repeat / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. ...Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / Toll-like receptor / Leucine Rich repeat / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / 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 3
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 3


Theoretical massNumber of molelcules
Total (without water)6,0431
Polymers6,0431
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 3


Mass: 6043.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR3 / Production host: Escherichia coli (E. coli) / References: UniProt: O15455

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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 HN(CO)CA
171isotropic13D HNCA
181isotropic13D (H)CCH-TOCSY
191isotropic13D (H)CCH-TOCSY
1101isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY aliphatic
1121isotropic13D (H)CCH-COSY aromatic
1131isotropic12D CBHD aromatic
2142anisotropic22D 1H-15N IPAP-HSQC
2152anisotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle1270 uM [U-13C; U-15N] protein, 128 mM [U-2H] DPC, 20 mM potassium phosphate, 4 mM TCEP, 0.05 % w/v sodium azide, 1 mM TSP, 95% H2O/5% D2O15N13C_sample95% H2O/5% D2O
micelle2220 uM [U-15N] protein, 142 mM DPC, 40 mM potassium phosphate, 4 mM TCEP, 0.05 % w/v sodium azide, 1 mM TSP, 37 mg/mL dGpG, 95% H2O/5% D2O15N_sample_forRDC95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
270 uMprotein[U-13C; U-15N]1
128 mMDPC[U-2H]1
20 mMpotassium phosphatenatural abundance1
4 mMTCEPnatural abundance1
0.05 % w/vsodium azidenatural abundance1
1 mMTSPnatural abundance1
220 uMprotein[U-15N]2
142 mMDPCnatural abundance2
40 mMpotassium phosphatenatural abundance2
4 mMTCEPnatural abundance2
0.05 % w/vsodium azidenatural abundance2
1 mMTSPnatural abundance2
37 mg/mLdGpGnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPH errPressure (kPa)Temperature (K)
150 mMconditions_main7.0 0.1AMBIENT atm318 K
290 mMconditions_forRDC7.0 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
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: 10

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