7BEQ

MicroED structure of the MyD88 TIR domain higher-order assembly


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

MyD88 TIR domain higher-order assembly interactions revealed by microcrystal electron diffraction and serial femtosecond crystallography.

Clabbers, M.T.B.Holmes, S.Muusse, T.W.Vajjhala, P.R.Thygesen, S.J.Malde, A.K.Hunter, D.J.B.Croll, T.I.Flueckiger, L.Nanson, J.D.Rahaman, M.H.Aquila, A.Hunter, M.S.Liang, M.Yoon, C.H.Zhao, J.Zatsepin, N.A.Abbey, B.Sierecki, E.Gambin, Y.Stacey, K.J.Darmanin, C.Kobe, B.Xu, H.Ve, T.

(2021) Nat Commun 12: 2578-2578

  • DOI: 10.1038/s41467-021-22590-6
  • Primary Citation of Related Structures:  
    7BEQ, 7BER, 7L6W

  • PubMed Abstract: 
  • MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MAL TIR ) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88 TIR ) ...

    MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MAL TIR ) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88 TIR ). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88 TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MAL TIR . We demonstrate via mutagenesis that the MyD88 TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88 TIR . Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.


    Organizational Affiliation

    Institute for Glycomics, Griffith University, Southport, Queensland, Australia. t.ve@griffith.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Myeloid differentiation primary response protein MyD88A151Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3.00 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 10.15785/SBGRID/814 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.06α = 90
b = 31.01β = 107.696
c = 54.3γ = 90
Software Package:
Software NamePurpose
phenix.refinerefinement
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2017-05333

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Database references