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- PDB-2ndh: NMR solution structure of MAL/TIRAP TIR domain (C116A) -

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Basic information

Entry
Database: PDB / ID: 2ndh
TitleNMR solution structure of MAL/TIRAP TIR domain (C116A)
ComponentsToll/interleukin-1 receptor domain-containing adapter protein
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of interleukin-15 production / TIRAP-dependent toll-like receptor 4 signaling pathway / regulation of interferon-beta production / cellular response to bacterial lipopeptide / positive regulation of toll-like receptor 3 signaling pathway / Toll-like receptor 4 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production ...positive regulation of interleukin-15 production / TIRAP-dependent toll-like receptor 4 signaling pathway / regulation of interferon-beta production / cellular response to bacterial lipopeptide / positive regulation of toll-like receptor 3 signaling pathway / Toll-like receptor 4 binding / positive regulation of toll-like receptor 2 signaling pathway / Toll-like receptor 2 binding / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production / myeloid cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / MyD88 deficiency (TLR2/4) / positive regulation of neutrophil chemotaxis / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / 3'-UTR-mediated mRNA stabilization / regulation of stress-activated MAPK cascade / regulation of innate immune response / cellular response to lipoteichoic acid / endocytic vesicle / canonical NF-kappaB signal transduction / signaling adaptor activity / positive regulation of B cell proliferation / extrinsic component of cytoplasmic side of plasma membrane / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-12 production / positive regulation of interleukin-8 production / protein kinase C binding / positive regulation of JNK cascade / positive regulation of protein-containing complex assembly / ruffle membrane / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / molecular adaptor activity / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / innate immune response / cell surface / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Toll-interleukin 1 receptor domain-containing adaptor protein, Tirap / TIR domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily
Similarity search - Domain/homology
Toll/interleukin-1 receptor domain-containing adapter protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsLavrencic, P. / Mobli, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Solution structure of the TLR adaptor MAL/TIRAP reveals an intact BB loop and supports MAL Cys91 glutathionylation for signaling.
Authors: Hughes, M.M. / Lavrencic, P. / Coll, R.C. / Ve, T. / Ryan, D.G. / Williams, N.C. / Menon, D. / Mansell, A. / Board, P.G. / Mobli, M. / Kobe, B. / O'Neill, L.A.J.
History
DepositionMay 27, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jun 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 1.5May 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/interleukin-1 receptor domain-containing adapter protein


Theoretical massNumber of molelcules
Total (without water)15,7271
Polymers15,7271
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Toll/interleukin-1 receptor domain-containing adapter protein / TIR domain-containing adapter protein / Adaptor protein Wyatt / MyD88 adapter-like protein / MyD88-2


Mass: 15726.875 Da / Num. of mol.: 1 / Fragment: TIR domain residues 79-221 / Mutation: C116A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIRAP, MAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P58753

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: NMR solution structure of the MAL/TIRAP TIR domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCO
1513D (H)CCH-TOCSY
1612D 1H-13C HSQC aliphatic
1712D 1H-13C HSQC aromatic
1813D 1H-15N NOESY
1913D HBHA(CO)NH
11013D HN(CO)CA

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Sample preparation

DetailsContents: 300 uM [U-99% 13C; U-99% 15N] protein, 20 mM TRIS, 5 % D2O, 200 mM sodium chloride, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMentity-1[U-99% 13C; U-99% 15N]1
20 mMTRIS-21
5 %D2O-31
200 mMsodium chloride-41
Sample conditionsIonic strength: 0.2 / pH: 8.6 / Pressure: ambient / Temperature: 291

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOSTALOS+Cornilescu, Delaglio and Baxchemical shift calculation
CCPNMR2.4CCPNchemical shift assignment
CCPNMR2.4CCPNdata analysis
CCPNMR2.4CCPNpeak picking
TopSpinBruker Biospinprocessing
Rowland_NMR_toolkit3JC Hoch et al.processing
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Automated NOE assignment
NMR constraintsNOE constraints total: 1363 / NOE intraresidue total count: 362 / NOE long range total count: 262 / NOE medium range total count: 317 / NOE sequential total count: 422 / Protein phi angle constraints total count: 106 / Protein psi angle constraints total count: 110
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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