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- PDB-2z5v: Solution structure of the TIR domain of human MyD88 -

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Basic information

Entry
Database: PDB / ID: 2z5v
TitleSolution structure of the TIR domain of human MyD88
ComponentsMyeloid differentiation primary response protein MyD88
KeywordsIMMUNE SYSTEM / signal transduction innate immunity / Cytoplasm / Immune response / Inflammatory response
Function / homology
Function and homology information


regulation of chemokine (C-X-C motif) ligand 1 production / MyD88 deficiency (TLR5) / TIR domain binding / ATP-dependent histone chaperone activity / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / regulation of chemokine (C-X-C motif) ligand 2 production / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response ...regulation of chemokine (C-X-C motif) ligand 1 production / MyD88 deficiency (TLR5) / TIR domain binding / ATP-dependent histone chaperone activity / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / regulation of chemokine (C-X-C motif) ligand 2 production / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response / response to molecule of fungal origin / positive regulation of lymphocyte proliferation / toll-like receptor 8 signaling pathway / response to peptidoglycan / regulation of neutrophil migration / positive regulation of interleukin-23 production / establishment of endothelial intestinal barrier / IRAK4 deficiency (TLR5) / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / Toll-like receptor binding / cellular response to oxidised low-density lipoprotein particle stimulus / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / toll-like receptor TLR6:TLR2 signaling pathway / interleukin-33-mediated signaling pathway / neutrophil activation involved in immune response / microglia differentiation / RIP-mediated NFkB activation via ZBP1 / interleukin-1 receptor binding / MyD88 deficiency (TLR2/4) / positive regulation of cytokine production involved in inflammatory response / death receptor binding / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / extrinsic component of cytoplasmic side of plasma membrane / 3'-UTR-mediated mRNA stabilization / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor 4 signaling pathway / extrinsic component of plasma membrane / positive regulation of macrophage cytokine production / type I interferon-mediated signaling pathway / skin development / defense response to protozoan / response to amine / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of interleukin-17 production / immunoglobulin mediated immune response / positive regulation of type I interferon production / phagocytosis / response to amino acid / positive regulation of chemokine production / JNK cascade / signaling adaptor activity / positive regulation of smooth muscle cell proliferation / response to interleukin-1 / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / cellular response to mechanical stimulus / : / positive regulation of interleukin-6 production / Interleukin-1 signaling / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / cellular response to lipopolysaccharide / ER-Phagosome pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / response to ethanol / defense response to virus / gene expression / molecular adaptor activity / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / endosome membrane / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / apoptotic process / positive regulation of gene expression / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Myeloid differentiation primary response protein MyD88 / MyD88, death domain / Toll/interleukin-1 receptor homology (TIR) domain / TIR domain / TIR domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Toll - interleukin 1 - resistance ...Myeloid differentiation primary response protein MyD88 / MyD88, death domain / Toll/interleukin-1 receptor homology (TIR) domain / TIR domain / TIR domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Death-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Myeloid differentiation primary response protein MyD88
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsOhnishi, H. / Tochio, H. / Hiroaki, H. / Kondo, N. / Kato, Z. / Shirakawa, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural basis for the multiple interactions of the MyD88 TIR domain in TLR4 signaling.
Authors: Ohnishi, H. / Tochio, H. / Kato, Z. / Orii, K.E. / Li, A. / Kimura, T. / Hiroaki, H. / Kondo, N. / Shirakawa, M.
History
DepositionJul 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myeloid differentiation primary response protein MyD88


Theoretical massNumber of molelcules
Total (without water)17,3871
Polymers17,3871
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Myeloid differentiation primary response protein MyD88


Mass: 17387.318 Da / Num. of mol.: 1 / Fragment: MyD88 TIR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYD88 / Plasmid: pGEX-5X-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: Q99836

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionsPressure: 1 atm / Temperature: 298 K

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Processing

NMR softwareName: CNS / Version: 1.1 / Classification: refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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