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- PDB-4dom: Crystal Structure of the TIR-domain of Human Myeloid Differentiat... -

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Basic information

Entry
Database: PDB / ID: 4dom
TitleCrystal Structure of the TIR-domain of Human Myeloid Differentiation Primary Response protein (MyD88)
ComponentsMyeloid differentiation primary response protein MyD88
KeywordsSIGNALING PROTEIN / MyD88_HUMAN / TIR-domain / Toll-Like Receptor / Adopter domain / Innate Immune signaling / TIRAP/MAL / Lysine Methylation
Function / homology
Function and homology information


regulation of chemokine (C-X-C motif) ligand 1 production / Toll binding / MyD88 deficiency (TLR5) / regulation of chemokine (C-X-C motif) ligand 2 production / ATP-dependent histone chaperone activity / neutrophil-mediated killing of bacterium / induced systemic resistance / leukocyte activation involved in inflammatory response / TIR domain binding / response to molecule of fungal origin ...regulation of chemokine (C-X-C motif) ligand 1 production / Toll binding / MyD88 deficiency (TLR5) / regulation of chemokine (C-X-C motif) ligand 2 production / ATP-dependent histone chaperone activity / neutrophil-mediated killing of bacterium / induced systemic resistance / leukocyte activation involved in inflammatory response / TIR domain binding / response to molecule of fungal origin / toll-like receptor 8 signaling pathway / positive regulation of lymphocyte proliferation / response to peptidoglycan / positive regulation of interleukin-23 production / establishment of endothelial intestinal barrier / regulation of neutrophil migration / IRAK4 deficiency (TLR5) / MyD88 dependent cascade initiated on endosome / cellular response to oxidised low-density lipoprotein particle stimulus / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / Toll signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / neutrophil activation involved in immune response / Toll-like receptor binding / interleukin-33-mediated signaling pathway / microglia differentiation / RIP-mediated NFkB activation via ZBP1 / positive regulation of cytokine production involved in inflammatory response / interleukin-1 receptor binding / death receptor binding / MyD88 deficiency (TLR2/4) / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / skin development / 3'-UTR-mediated mRNA stabilization / positive regulation of NLRP3 inflammasome complex assembly / extrinsic component of plasma membrane / type I interferon-mediated signaling pathway / positive regulation of interleukin-17 production / defense response to protozoan / response to amine / immunoglobulin mediated immune response / positive regulation of type I interferon production / response to amino acid / phagocytosis / signaling adaptor activity / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / response to interleukin-1 / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / positive regulation of smooth muscle cell proliferation / response to organic cyclic compound / Interleukin-1 signaling / cellular response to mechanical stimulus / positive regulation of interleukin-6 production / : / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / positive regulation of NF-kappaB transcription factor activity / gene expression / ER-Phagosome pathway / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / cellular response to lipopolysaccharide / molecular adaptor activity / cell surface receptor signaling pathway / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsJiang, J.S. / Snyder, G.A. / Xiao, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Molecular mechanisms for the subversion of MyD88 signaling by TcpC from virulent uropathogenic Escherichia coli.
Authors: Snyder, G.A. / Cirl, C. / Jiang, J. / Chen, K. / Waldhuber, A. / Smith, P. / Rommler, F. / Snyder, N. / Fresquez, T. / Durr, S. / Tjandra, N. / Miethke, T. / Xiao, T.S.
History
DepositionFeb 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2May 8, 2013Group: Database references
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)16,7191
Polymers16,7191
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.415, 57.991, 62.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myeloid differentiation primary response protein MyD88


Mass: 16718.621 Da / Num. of mol.: 1 / Fragment: TIR domain, UNP residues 157-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYD88 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99836
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG 8000, 0.1M Immidazole pH 8.0, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2007
RadiationMonochromator: Si Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.798→50 Å / Num. all: 11846 / Num. obs: 11360 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 21.04 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 11.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.9 / Num. unique all: 952 / % possible all: 81

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7_650)refinement
AMoREphasing
CNSrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JS7

2js7


Resolution: 1.798→42.509 Å / SU ML: 0.16 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 560 5.18 %RANDOM
Rwork0.1796 ---
all0.1817 11360 --
obs0.1817 10821 91.58 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.311 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso mean: 28.31 Å2
Baniso -1Baniso -2Baniso -3
1--6.6799 Å2-0 Å20 Å2
2---1.2192 Å20 Å2
3---7.8991 Å2
Refinement stepCycle: LAST / Resolution: 1.798→42.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 0 102 1271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061198
X-RAY DIFFRACTIONf_angle_d1.1071618
X-RAY DIFFRACTIONf_dihedral_angle_d16.828459
X-RAY DIFFRACTIONf_chiral_restr0.092177
X-RAY DIFFRACTIONf_plane_restr0.007201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.798-1.97930.25621180.21382140X-RAY DIFFRACTION78
1.9793-2.26570.23351240.17162618X-RAY DIFFRACTION94
2.2657-2.85450.23131490.17672728X-RAY DIFFRACTION98
2.8545-42.52090.20171690.17752775X-RAY DIFFRACTION96

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