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- PDB-2mk9: Spatial structure of the dimeric transmembrane domain of Toll-lik... -

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Basic information

Entry
Database: PDB / ID: 2mk9
TitleSpatial structure of the dimeric transmembrane domain of Toll-like receptor 3
ComponentsToll-like receptor 3
KeywordsIMMUNE SYSTEM / transmembrane domain / dimer
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 / positive regulation of cytokine production involved in inflammatory response / endolysosome membrane / hyperosmotic response / Trafficking and processing of endosomal TLR / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / response to exogenous dsRNA / cellular response to exogenous dsRNA / negative regulation of osteoclast differentiation / positive regulation of interferon-alpha production / cellular response to interferon-beta / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / 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 interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / male gonad development / positive regulation of angiogenesis / positive regulation of type II interferon production / transmembrane signaling receptor activity / cellular response to xenobiotic stimulus / positive regulation of tumor necrosis factor production / double-stranded RNA binding / 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 / endoplasmic reticulum membrane / positive regulation of gene expression / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / membrane / identical protein binding / 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 / simulated annealing
Model detailsfewest violations, model1
AuthorsMineev, K.S. / Goncharuk, S.A. / Arseniev, A.S.
CitationJournal: Febs Lett. / Year: 2014
Title: Toll-like receptor 3 transmembrane domain is able to perform various homotypic interactions: An NMR structural study.
Authors: Mineev, K.S. / Goncharuk, S.A. / Arseniev, A.S.
History
DepositionFeb 4, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 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
B: Toll-like receptor 3


Theoretical massNumber of molelcules
Total (without water)8,1802
Polymers8,1802
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Toll-like receptor 3 /


Mass: 4089.947 Da / Num. of mol.: 2 / Fragment: transmembrane domain (UNP residues 698-730)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR3 / Plasmid: pET22b / Production host: cell-free synthesis (others) / References: UniProt: O15455

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HNCO
1413D HN(CO)CA
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D (H)CCH-COSY
19113C/15N-filtered NOESY

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Sample preparation

DetailsContents: 0.8 mM Toll-like receptor 3, 1.2 mM [U-98% 13C; U-98% 15N] Toll-like receptor 3, 20 mM potassium phosphate, 1 mM sodium azide, 200 mM [U-99% 2H] DPC, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMToll-like receptor 3-11
1.2 mMToll-like receptor 3-2[U-98% 13C; U-98% 15N]1
20 mMpotassium phosphate-31
1 mMsodium azide-41
200 mMDPC-5[U-99% 2H]1
Sample conditionsIonic strength: 20 / pH: 7.5 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
CARA1.8.5Keller and Wuthrichchemical shift assignment
CARA1.8.5Keller and Wuthrichdata analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
TALOS+Cornilescu, Delaglio and Baxdata analysis
qMDD2.1Orekhov, Mayzelprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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