8S78 | pdb_00008s78

MicroED Structure of TLR2 TIR domain-induced MyD88 TIR domain higher-order assembly


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.267 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.269 (DCC) 
  • R-Value Observed: 
    0.256 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Microcrystal electron diffraction structure of Toll-like receptor 2 TIR-domain-nucleated MyD88 TIR-domain higher-order assembly.

Li, Y.Pacoste, L.C.Gu, W.Thygesen, S.J.Stacey, K.J.Ve, T.Kobe, B.Xu, H.Nanson, J.D.

(2024) Acta Crystallogr D Struct Biol 80: 699-712

  • DOI: https://doi.org/10.1107/S2059798324008210
  • Primary Citation of Related Structures:  
    8S78

  • PubMed Abstract: 

    Eukaryotic TIR (Toll/interleukin-1 receptor protein) domains signal via TIR-TIR interactions, either by self-association or by interaction with other TIR domains. In mammals, TIR domains are found in Toll-like receptors (TLRs) and cytoplasmic adaptor proteins involved in pro-inflammatory signaling. Previous work revealed that the MAL TIR domain (MAL TIR ) nucleates the assembly of MyD88 TIR into crystalline arrays in vitro. A microcrystal electron diffraction (MicroED) structure of the MyD88 TIR assembly has previously been solved, revealing a two-stranded higher-order assembly of TIR domains. In this work, it is demonstrated that the TIR domain of TLR2, which is reported to signal as a heterodimer with either TLR1 or TLR6, induces the formation of crystalline higher-order assemblies of MyD88 TIR in vitro, whereas TLR1 TIR and TLR6 TIR do not. Using an improved data-collection protocol, the MicroED structure of TLR2 TIR -induced MyD88 TIR microcrystals was determined at a higher resolution (2.85 Å) and with higher completeness (89%) compared with the previous structure of the MAL TIR -induced MyD88 TIR assembly. Both assemblies exhibit conformational differences in several areas that are important for signaling (for example the BB loop and CD loop) compared with their monomeric structures. These data suggest that TLR2 TIR and MAL TIR interact with MyD88 in an analogous manner during signaling, nucleating MyD88 TIR assemblies unidirectionally.


  • Organizational Affiliation
    • Institute of Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myeloid differentiation primary response protein MyD88151Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: MYD88
UniProt & NIH Common Fund Data Resources
Find proteins for Q99836 (Homo sapiens)
Explore Q99836 
Go to UniProtKB:  Q99836
PHAROS:  Q99836
GTEx:  ENSG00000172936 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99836
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.85 Å
  • R-Value Free:  0.267 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.269 (DCC) 
  • R-Value Observed: 0.256 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.07α = 90
b = 30.64β = 107.81
c = 53.67γ = 90
Software Package:
Software NamePurpose
XDSdata processing
XSCALEdata scaling
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX20.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1071659, 1107804 and 1160570
Australian Research Council (ARC)AustraliaARC FL180100109
Swedish Research CouncilSweden2019-00815
Knut and Alice Wallenberg FoundationSweden2018.0237

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Database references