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- PDB-4eo7: Crystal structure of the TIR domain of human myeloid differentiat... -

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Basic information

Entry
Database: PDB / ID: 4eo7
TitleCrystal structure of the TIR domain of human myeloid differentiation primary response protein 88.
ComponentsMyeloid differentiation primary response protein MyD88
KeywordsPROTEIN BINDING / Adapter Protein / toll like receptor / BETA-ALPHA-BETA FOLD / PARALLEL BETA SHEET / TIR-Domain / Innate immune signaling / Signaling protein / TIRAP/MAL
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 / response to peptidoglycan / toll-like receptor 8 signaling pathway / positive regulation of interleukin-23 production / regulation of neutrophil migration / IRAK4 deficiency (TLR5) / establishment of endothelial intestinal barrier / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / cellular response to oxidised low-density lipoprotein particle stimulus / Toll signaling pathway / Toll-like receptor binding / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / 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 / positive regulation of cytokine production involved in inflammatory response / MyD88 deficiency (TLR2/4) / death receptor binding / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / 3'-UTR-mediated mRNA stabilization / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / extrinsic component of plasma membrane / skin development / type I interferon-mediated signaling pathway / response to amine / defense response to protozoan / 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 / p75NTR recruits signalling complexes / response to interleukin-1 / 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 smooth muscle cell proliferation / positive regulation of JNK cascade / positive regulation of NF-kappaB transcription factor activity / positive regulation of interleukin-6 production / cellular response to mechanical stimulus / Interleukin-1 signaling / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / ER-Phagosome pathway / cellular response to lipopolysaccharide / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / response to ethanol / defense response to virus / molecular adaptor activity / gene expression / positive regulation of canonical NF-kappaB signal transduction / 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: 1.449 Å
AuthorsSnyder, G.A. / Cirl, C. / Jiang, J.S. / Chen, P. / Smith, T. / Xiao, T.S.
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
DepositionApr 13, 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 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myeloid differentiation primary response protein MyD88
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8052
Polymers16,7811
Non-polymers241
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.876, 56.810, 66.664
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: 16780.627 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: 25% PEG 3350, 0.1M BIS-TRIS pH 6.5,0.2M NaCl, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 3, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.449→50 Å / Num. obs: 23051 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.449→1.48 Å / % possible all: 80.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DOM

4dom


Resolution: 1.449→43.239 Å / SU ML: 0.16 / σ(F): 1.34 / σ(I): 2 / Phase error: 19.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 1162 5.06 %Random
Rwork0.1681 ---
obs0.17 22962 94.98 %-
all-23051 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.691 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.554 Å2-0 Å20 Å2
2---0.2806 Å2-0 Å2
3---0.2313 Å2
Refinement stepCycle: LAST / Resolution: 1.449→43.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 1 232 1406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061262
X-RAY DIFFRACTIONf_angle_d0.9541724
X-RAY DIFFRACTIONf_dihedral_angle_d13.623501
X-RAY DIFFRACTIONf_chiral_restr0.069193
X-RAY DIFFRACTIONf_plane_restr0.005219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.449-1.51540.29711230.22972267X-RAY DIFFRACTION81
1.5154-1.59530.2761340.19912429X-RAY DIFFRACTION87
1.5953-1.69520.24811420.18162697X-RAY DIFFRACTION95
1.6952-1.82610.19531480.16892807X-RAY DIFFRACTION99
1.8261-2.00990.20461510.16962818X-RAY DIFFRACTION99
2.0099-2.30070.20191510.16232864X-RAY DIFFRACTION99
2.3007-2.89860.18961530.16112894X-RAY DIFFRACTION100
2.8986-43.25840.19531600.15843024X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7936-1.66631.79011.7909-1.17651.60780.16590.0862-0.1803-0.09610.09020.14110.1895-0.1883-0.1670.0713-0.0262-0.00160.09190.0340.06992.46731.06826.6609
21.38860.0652-0.48694.2193-0.66122.66840.01230.05910.1319-0.0129-0.02460.0795-0.1923-0.09730.03450.04330.00650.00240.03150.00340.069611.46479.872914.7297
32.69362.5759-2.48795.0722-4.46543.95860.08920.04120.1480.03380.13220.2946-0.0765-0.1596-0.15240.06530.0061-0.01540.08340.01090.06966.826.72114.8782
41.51220.54220.24482.94653.37464.1776-0.02640.0230.1247-0.30470.00110.264-0.2548-0.38920.02650.05660.0266-0.01780.12230.01020.10620.84736.006312.4647
53.87251.4136-1.90272.5657-0.08572.62180.0902-0.1319-0.07040.1259-0.13210.26120.224-0.210.04270.1283-0.073-0.080.08710.02550.1922.0405-9.71768.8214
62.53790.93790.59611.65931.06990.70150.0354-0.0729-0.10850.0746-0.0073-0.02660.0902-0.0471-0.02390.06220.00090.00050.01910.01380.054915.0984-2.904115.7621
71.21090.49940.29713.45620.70441.4938-0.01140.068-0.0966-0.19810.00120.01120.11530.0260.00740.0860.0058-0.00050.0406-0.0050.088415.3399-9.177811.1713
82.27780.1390.69913.6061-1.16833.06130.02020.0371-0.24040.07680.0297-0.29270.32590.19520.00140.06870.0051-0.04430.02330.00450.096424.5515-0.426221.3484
95.112-1.82870.81175.7699-4.5595.11430.34380.0666-0.0344-0.2488-0.2244-0.3306-0.06810.2719-0.11390.1550.02530.00710.0652-0.01030.125224.6078-9.352211.4496
103.49141.8422.06573.54831.09683.4723-0.05430.2307-0.0615-0.17170.0668-0.10850.03680.2163-0.03480.05540.00440.02570.04630.00470.052521.12157.58075.0955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 153:168)
2X-RAY DIFFRACTION2chain 'A' and (resseq 169:183)
3X-RAY DIFFRACTION3chain 'A' and (resseq 184:195)
4X-RAY DIFFRACTION4chain 'A' and (resseq 196:208)
5X-RAY DIFFRACTION5chain 'A' and (resseq 209:215)
6X-RAY DIFFRACTION6chain 'A' and (resseq 216:230)
7X-RAY DIFFRACTION7chain 'A' and (resseq 231:256)
8X-RAY DIFFRACTION8chain 'A' and (resseq 257:265)
9X-RAY DIFFRACTION9chain 'A' and (resseq 266:272)
10X-RAY DIFFRACTION10chain 'A' and (resseq 273:296)

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