7BER

SFX structure of the MyD88 TIR domain higher-order assembly (solved, rebuilt and refined using an identical protocol to the MicroED structure of the MyD88 TIR domain higher-order assembly)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/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 ). 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

    Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myeloid differentiation primary response protein MyD88151Homo 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
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.4α = 90
b = 31.5β = 107.4
c = 54.5γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
CrystFELdata scaling
Aimlessdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2017-05333
Australian Research Council (ARC)AustraliaCE140100011

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
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-31
    Changes: Refinement description