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- PDB-8s78: MicroED Structure of TLR2 TIR domain-induced MyD88 TIR domain hig... -

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Basic information

Entry
Database: PDB / ID: 8s78
TitleMicroED Structure of TLR2 TIR domain-induced MyD88 TIR domain higher-order assembly
ComponentsMyeloid differentiation primary response protein MyD88
KeywordsIMMUNE SYSTEM / MICROED / MYD88 / TIR DOMAIN / HIGHER-ORDER ASSEMBLY / TLR2
Function / homology
Function and homology information


regulation of chemokine (C-X-C motif) ligand 1 production / MyD88 deficiency (TLR5) / TIR domain binding / regulation of chemokine (C-X-C motif) ligand 2 production / ATP-dependent histone chaperone activity / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / 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 / regulation of chemokine (C-X-C motif) ligand 2 production / ATP-dependent histone chaperone activity / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / 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 / establishment of endothelial intestinal barrier / positive regulation of interleukin-23 production / regulation of neutrophil migration / IRAK4 deficiency (TLR5) / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / Toll signaling pathway / MyD88 cascade initiated on plasma membrane / cellular response to oxidised low-density lipoprotein particle stimulus / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / Toll-like receptor binding / 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 / death receptor binding / positive regulation of cytokine production involved in inflammatory response / interleukin-1 receptor binding / MyD88 deficiency (TLR2/4) / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / positive regulation of macrophage cytokine production / IRAK4 deficiency (TLR2/4) / 3'-UTR-mediated mRNA stabilization / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / extrinsic component of plasma membrane / skin development / type I interferon-mediated signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / defense response to protozoan / response to amine / positive regulation of interleukin-17 production / immunoglobulin mediated immune response / positive regulation of type I interferon production / response to amino acid / phagocytosis / positive regulation of chemokine production / signaling adaptor activity / lipopolysaccharide-mediated signaling pathway / JNK cascade / 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 smooth muscle cell proliferation / positive regulation of JNK cascade / : / 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 / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / cellular response to lipopolysaccharide / gene expression / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / defense response to virus / response to ethanol / cell surface receptor signaling pathway / endosome membrane / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / positive regulation of gene expression / apoptotic process / 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 / 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 ...Myeloid differentiation primary response protein MyD88 / MyD88, death 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
Similarity search - Domain/homology
Myeloid differentiation primary response protein MyD88
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 2.85 Å
AuthorsLi, Y. / Pacoste, L. / Xu, H. / Kobe, B.
Funding support Australia, Sweden, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1071659, 1107804 and 1160570 Australia
Australian Research Council (ARC)ARC FL180100109 Australia
Swedish Research Council2019-00815 Sweden
Knut and Alice Wallenberg Foundation2018.0237 Sweden
CitationJournal: To Be Published
Title: Structure of TLR2 TIR domain-induced MyD88 TIR domain higher-order assembly revealed by microcrystal electron diffraction (MicroED)
Authors: Li, Y. / Pacoste, L. / Xu, H.
History
DepositionFeb 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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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)17,8341
Polymers17,8341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.070, 30.640, 53.670
Angle α, β, γ (deg.)90.000, 107.810, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Myeloid differentiation primary response protein MyD88


Mass: 17833.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: MYD88 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99836
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Myeloid differentiation primary response 88 Toll/interleukin-1 receptor/resistance domain (MyD88 TIR).
Type: COMPLEX
Details: Myeloid differentiation primary response 88 Toll/interleukin-1 receptor/resistance domain (MyD88 TIR)
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 17.83 kDa/nm / Experimental value: NO
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5 / Details: TLR2 TIR protein, 10 mM HEPES pH 7.5, 150 mM NaCl
SpecimenConc.: 1.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 20 mA / Grid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Temperature (min): 77 K
Image recordingAverage exposure time: 0.85 sec. / Electron dose: 0.138 e/Å2 / Film or detector model: FEI CETA (4k x 4k)
Image scansWidth: 4000 / Height: 4000
EM diffraction shellResolution: 2.85→2.95 Å / Fourier space coverage: 83 % / Multiplicity: 8.2 / Num. of structure factors: 289 / Phase residual: 40.23 °
EM diffraction statsFourier space coverage: 89.2 % / High resolution: 2.85 Å / Num. of intensities measured: 3253 / Num. of structure factors: 3253 / Phase error rejection criteria: 0 / Rmerge: 0.51
ReflectionBiso Wilson estimate: 70.01 Å2

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Processing

Software
NameClassification
XDSdata processing
XSCALEdata scaling
EM software
IDNameVersionCategory
6PHENIX20.1model fitting
8PHENIX20.1model refinement
9PHENIX20.1molecular replacement
EM 3D crystal entity∠α: 90 ° / ∠β: 107.81 ° / ∠γ: 90 ° / A: 98.07 Å / B: 30.64 Å / C: 53.67 Å / Space group name: C121 / Space group num: 5
CTF correctionType: NONE
3D reconstructionResolution: 2.85 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 64.46
Atomic model buildingPDB-ID: 7beq

7beq


Accession code: 7beq / Source name: PDB / Type: experimental model
RefinementResolution: 2.85→19.99 Å / SU ML: 0.0856 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.795
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2669 153 4.7 %
Rwork0.2554 3100 -
obs0.2558 3253 87.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.46 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0031160
ELECTRON CRYSTALLOGRAPHYf_angle_d0.61731567
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0433174
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0056196
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d16.3441442
LS refinement shellResolution: 2.85→19.99 Å
RfactorNum. reflection% reflection
Rfree0.2669 153 -
Rwork0.2554 3100 -
obs--87.78 %
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON CRYSTALLOGRAPHY

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)
10.379635760466-0.4416780933110.8351095515854.180127994340.1386633725092.19992481348-0.2473219663850.02748121188120.04980780856820.4192139729920.2352881929430.385324693030.225860008317-0.1152556497620.04998654141550.507937548249-0.04704213983140.05137514887060.601562274003-0.04431879874830.51349987938412.7402304377-2.075366279329.37681877549
23.45875844435-1.62385720074-0.9711464708932.49254426299-0.7169068408732.54146729111-0.114074474975-0.115692390224-0.01344814038120.07015599981540.09856286977260.1825063053950.4022526318190.0727357932594-0.00284159633510.8100687122020.00675781420271-0.1485201563070.3621151144590.01320864046040.59583691475516.8700589547-13.164610041613.2324795395
Refinement TLS group

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 159 through 230 )159 - 2301 - 72
22chain 'A' and (resid 231 through 296 )231 - 29673 - 138

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