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- PDB-5nao: NMR structure of TLR4 transmembrane domain (624-657) in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 5nao
TitleNMR structure of TLR4 transmembrane domain (624-657) in DPC micelles
ComponentsToll-like receptor 4
KeywordsSIGNALING PROTEIN / Toll-like receptor / PROTEIN RECEPTOR / transmembrane domain / PROTEIN
Function / homology
Function and homology information


detection of fungus / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / lipopolysaccharide immune receptor activity / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of matrix metallopeptidase secretion / lipopolysaccharide receptor complex / detection of lipopolysaccharide / regulation of dendritic cell cytokine production ...detection of fungus / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / lipopolysaccharide immune receptor activity / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of matrix metallopeptidase secretion / lipopolysaccharide receptor complex / detection of lipopolysaccharide / regulation of dendritic cell cytokine production / MyD88-independent TLR4 cascade / I-kappaB phosphorylation / negative regulation of interleukin-23 production / TRIF-mediated programmed cell death / cellular response to oxidised low-density lipoprotein particle stimulus / wound healing involved in inflammatory response / B cell proliferation involved in immune response / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / positive regulation of stress-activated MAPK cascade / intestinal epithelial structure maintenance / positive regulation of interleukin-1 production / macrophage activation / Regulation of TLR by endogenous ligand / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / microglia differentiation / NAD+ nucleosidase activity, cyclic ADP-ribose generating / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / positive regulation of platelet activation / negative regulation of interleukin-17 production / positive regulation of cytokine production involved in inflammatory response / MyD88 deficiency (TLR2/4) / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of cold-induced thermogenesis / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / positive regulation of macrophage cytokine production / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / T-helper 1 type immune response / toll-like receptor signaling pathway / positive regulation of smooth muscle cell migration / positive regulation of reactive oxygen species biosynthetic process / positive regulation of NLRP3 inflammasome complex assembly / RSV-host interactions / negative regulation of osteoclast differentiation / cellular response to lipoteichoic acid / negative regulation of interleukin-6 production / negative regulation of type II interferon production / positive regulation of interferon-alpha production / Respiratory syncytial virus (RSV) attachment and entry / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / phagocytic cup / phagocytosis / stress-activated MAPK cascade / positive regulation of chemokine production / ruffle / JNK cascade / cellular response to platelet-derived growth factor stimulus / positive regulation of B cell proliferation / nitric oxide biosynthetic process / positive regulation of interleukin-12 production / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / ERK1 and ERK2 cascade / positive regulation of MAP kinase activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of interferon-beta production / lipopolysaccharide-mediated signaling pathway / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / positive regulation of interleukin-1 beta production / IKK complex recruitment mediated by RIP1 / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / positive regulation of JNK cascade / lipopolysaccharide binding / Heme signaling / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of type II interferon production / cellular response to mechanical stimulus / positive regulation of inflammatory response / cellular response to amyloid-beta / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / signaling receptor activity / amyloid-beta binding / ER-Phagosome pathway / cellular response to lipopolysaccharide
Similarity search - Function
Toll-like receptor / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / TIR domain / Leucine Rich repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily ...Toll-like receptor / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / TIR domain / Leucine Rich repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMineev, K.S. / Goncharuk, S.A. / Goncharuk, M.V. / Arseniev, A.S.
CitationJournal: Sci Rep / Year: 2017
Title: Spatial structure of TLR4 transmembrane domain in bicelles provides the insight into the receptor activation mechanism.
Authors: Mineev, K.S. / Goncharuk, S.A. / Goncharuk, M.V. / Volynsky, P.E. / Novikova, E.V. / Aresinev, A.S.
History
DepositionFeb 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toll-like receptor 4


Theoretical massNumber of molelcules
Total (without water)3,9041
Polymers3,9041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3830 Å2
MethodPISA
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 4 / hToll


Mass: 3903.716 Da / Num. of mol.: 1 / Fragment: UNP residues 623-657
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR4 / Production host: Escherichia coli (E. coli) / References: UniProt: O00206

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HNCA
131isotropic13D 1H-15N NOESY
141isotropic13D 1H-13C NOESY aliphatic
151isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: micelle
Contents: 1.0 mM [U-100% 13C; U-100% 15N] TLR4-TM, 100 mM [U-99% 2H] DPC, 20 mM sodium phosphate, 0.01 % sodium azide, 90% H2O/10% D2O
Details: sample in DPC micelles / Label: 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMTLR4-TM[U-100% 13C; U-100% 15N]1
100 mMDPC[U-99% 2H]1
20 mMsodium phosphatenatural abundance1
0.01 %sodium azidenatural abundance1
Sample conditionsIonic strength: 20 mM / Label: 1 / pH: 6 / Pressure: AMBIENT atm / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.1Keller and Wuthrichchemical shift assignment
TopSpin3.5Bruker Biospinprocessing
RefinementMethod: torsion angle dynamics / 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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