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- PDB-5nam: NMR structure of TLR4 transmembrane domain (624-670) in DMPG/DHPC... -

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Basic information

Entry
Database: PDB / ID: 5nam
TitleNMR structure of TLR4 transmembrane domain (624-670) in DMPG/DHPC bicelles
ComponentsToll-like receptor 4
KeywordsSIGNALING PROTEIN / Toll-like receptor / PROTEIN RECEPTOR / transmembrane domain / PROTEIN
Function / homology
Function and homology information


nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / detection of fungus / 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 / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / regulation of dendritic cell cytokine production / detection of lipopolysaccharide ...nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / detection of fungus / 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 / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / regulation of dendritic cell cytokine production / detection of lipopolysaccharide / intestinal epithelial structure maintenance / MyD88-independent TLR4 cascade / TRIF-mediated programmed cell death / I-kappaB phosphorylation / negative regulation of interleukin-23 production / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to oxidised low-density lipoprotein particle stimulus / wound healing involved in inflammatory response / Caspase activation via Death Receptors in the presence of ligand / B cell proliferation involved in immune response / nucleotide-binding oligomerization domain containing 1 signaling pathway / Toll Like Receptor 4 (TLR4) Cascade / positive regulation of interleukin-1 production / positive regulation of stress-activated MAPK cascade / macrophage activation / Regulation of TLR by endogenous ligand / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / microglia differentiation / nucleotide-binding oligomerization domain containing 2 signaling pathway / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of MHC class II biosynthetic process / negative regulation of interleukin-17 production / positive regulation of platelet activation / positive regulation of cytokine production involved in inflammatory response / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of macrophage activation / positive regulation of chemokine (C-X-C motif) ligand 2 production / MyD88 deficiency (TLR2/4) / positive regulation of macrophage cytokine production / negative regulation of cold-induced thermogenesis / MyD88-dependent toll-like receptor signaling pathway / positive regulation of reactive oxygen species biosynthetic process / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / T-helper 1 type immune response / toll-like receptor signaling pathway / RSV-host interactions / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / negative regulation of osteoclast differentiation / positive regulation of nitric-oxide synthase biosynthetic process / cellular response to lipoteichoic acid / negative regulation of interleukin-6 production / Respiratory syncytial virus (RSV) attachment and entry / phagocytic cup / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / positive regulation of interferon-alpha production / phagocytosis / stress-activated MAPK cascade / positive regulation of chemokine production / positive regulation of B cell proliferation / JNK cascade / lipopolysaccharide-mediated signaling pathway / ruffle / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / nitric oxide biosynthetic process / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of interferon-beta production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of JNK cascade / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / Heme signaling / negative regulation of ERK1 and ERK2 cascade / 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 / cellular response to amyloid-beta / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / gene expression / ER-Phagosome pathway
Similarity search - Function
Toll-like receptor / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / 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 / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / 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 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.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RSF14-14-00573 Russian Federation
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 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 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)5,2821
Polymers5,2821
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4990 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: 5282.465 Da / Num. of mol.: 1 / Fragment: UNP residues 623-670
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL23 / 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
111isotropic22D 1H-15N HSQC
121isotropic23D HNCA
131isotropic23D HNCO
141isotropic13D HN(CO)CA
151isotropic23D (H)CCH-TOCSY
191isotropic23D (H)CCH-COSY
181isotropic23D 1H-15N NOESY
171isotropic13D 1H-13C NOESY
1112isotropic13D HNCA
1102isotropic13D HN(CO)CA
1134isotropic13D HNCA
1124isotropic13D HN(CO)CA

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
bicelle10.5 mM [U-13C; U-15N] TLR4-TM, 71 mM DHPC, 29 mM DMPG, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2Osample in DMPG/DHPC bicellesDMPG90% H2O/10% D2O
bicelle20.5 mM [U-13C; U-15N] TLR4-TM, 71 mM DHPC, 29 mM DMPC, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2Osample in DMPC/DHPC bicellesDMPC90% H2O/10% D2O
micelle40.5 mM [U-13C; U-15N] TLR4-TM, 50 mM [U-2H] DPC, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2Osample in DPC micellesDPC90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTLR4-TM[U-13C; U-15N]1
71 mMDHPCnatural abundance1
29 mMDMPGnatural abundance1
10 mMimidazolenatural abundance1
0.01 %sodium azidenatural abundance1
0.5 mMTLR4-TM[U-13C; U-15N]2
71 mMDHPCnatural abundance2
29 mMDMPCnatural abundance2
10 mMimidazolenatural abundance2
0.01 %sodium azidenatural abundance2
0.5 mMTLR4-TM[U-13C; U-15N]4
50 mMDPC[U-2H]4
10 mMimidazolenatural abundance4
0.01 %sodium azidenatural abundance4
Sample conditionsIonic strength: 10 mM / Label: conditions_1 / pH: 6.0 / PH err: 0.1 / Pressure: AMBIENT atm / Temperature: 313 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
CYANA3.97Guntert, 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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