7BEQ

MicroED structure of the MyD88 TIR domain higher-order assembly

• PDB DOI:  https://doi.org/10.2210/pdb7BEQ/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-24 Released: 2021-03-10 
• Deposition Author(s): Clabbers, M.T.B., Holmes, S., Muusse, T.W., Vajjhala, P., Thygesen, S.J., Malde, A.K., Hunter, D.J.B., Croll, T.I., 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., Darmanin, C., Kobe, B., Xu, H., Ve, T.
• Funding Organization(s): Swedish Research Council

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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 

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

• PubMed: 33972532 
• 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.

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Organizational Affiliation: 

Institute for Glycomics, Griffith University, Southport, Queensland, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.83 kDa 
• Atom Count: 1,133 
• Modelled Residue Count: 138 
• Deposited Residue Count: 151 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloid differentiation primary response protein MyD88	A	151	Homo sapiens	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

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: https://doi.org/10.15785/SBGRID/814

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.06	α = 90
b = 31.01	β = 107.696
c = 54.3	γ = 90

Software Package:

Software Name	Purpose
phenix.refine	refinement
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-10 
Deposition Author(s): Clabbers, M.T.B., Holmes, S., Muusse, T.W., Vajjhala, P., Thygesen, S.J., Malde, A.K., Hunter, D.J.B., Croll, T.I., 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., Darmanin, C., Kobe, B., Xu, H., Ve, T.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2017-05333

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2021-05-26
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references