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- PDB-8ar2: Solution structure of TLR5 transmembrane and cytoplasmic juxtamem... -

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Basic information

Entry
Database: PDB / ID: 8ar2
TitleSolution structure of TLR5 transmembrane and cytoplasmic juxtamembrane regions
ComponentsToll-like receptor 5
KeywordsMEMBRANE PROTEIN / PROTEIN
Function / homology
Function and homology information


Toll Like Receptor 5 (TLR5) Cascade / toll-like receptor 5 signaling pathway / MyD88 deficiency (TLR5) / IRAK4 deficiency (TLR5) / MyD88 cascade initiated on plasma membrane / interleukin-1 receptor binding / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interleukin-8 production / cellular response to mechanical stimulus ...Toll Like Receptor 5 (TLR5) Cascade / toll-like receptor 5 signaling pathway / MyD88 deficiency (TLR5) / IRAK4 deficiency (TLR5) / MyD88 cascade initiated on plasma membrane / interleukin-1 receptor binding / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interleukin-8 production / cellular response to mechanical stimulus / transmembrane signaling receptor activity / signaling receptor activity / inflammatory response / innate immune response / plasma membrane
Similarity search - Function
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 repeat, SDS22-like subfamily / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...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 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsShabalkina, A.V. / Kornilov, F.D. / 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 5


Theoretical massNumber of molelcules
Total (without water)5,8801
Polymers5,8801
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 5 / Toll/interleukin-1 receptor-like protein 3


Mass: 5880.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR5, TIL3 / Production host: Escherichia coli (E. coli) / References: UniProt: O60602

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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 (H)CCH-TOCSY constant time
1101isotropic13D 1H-15N NOESY
1111isotropic13D 1H-13C NOESY aliphatic
1121isotropic13D 1H-13C NOESY aliphatic constant time
1131isotropic12D CBHD aromatic
1141isotropic13D (H)CCH-COSY aromatic
1151isotropic12D CGCO
1161isotropic12D CGN
2172anisotropic22D 1H-15N HSQC
2182anisotropic22D 1H-15N IPAP-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle11000 uM [U-13C; U-15N] protein, 220 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
micelle2180 uM [U-15N] protein, 40 mM DPC, 30 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
1000 uMprotein[U-13C; U-15N]1
220 mMDPC[U-2H]1
20 mMpotassium phosphatenatural abundance1
4 mMTCEPnatural abundance1
0.05 % w/vsodium azidenatural abundance1
1 mMTSPnatural abundance1
180 uMprotein[U-15N]2
40 mMDPCnatural abundance2
30 mMpotassium phosphatenatural abundance2
4 mMTCEPnatural abundance2
0.05 % w/vsodium azidenatural abundance2
1 mMTSPnatural abundance2
30 mg/mLdGpGnatural abundance2
100 mMpotassium chloridenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPH errPressure (kPa)Temperature (K)
150 mMconditions_main6.0 0.1AMBIENT atm313 K
2160 mMconditions_RDC6.0 0.1AMBIENT atm318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III6002

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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
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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