7L6W | pdb_00007l6w

SFX structure of the MyD88 TIR domain higher-order assembly

• PDB DOI: https://doi.org/10.2210/pdb7L6W/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., 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.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.288 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

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 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: 
• Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden.
Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, USA.
Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.
Institute for Glycomics, Griffith University, Southport, Queensland, Australia.
EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, New South Wales, Australia.
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA.
Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia.
Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia. [e-mail].
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia. [e-mail].
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia. [e-mail].
Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia. [e-mail].
Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden. [e-mail].
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: 16.21 kDa 
• Atom Count: 1,183 
• Modeled Residue Count: 138 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloid differentiation primary response protein MyD88	A	138	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 GTEx:  ENSG00000172936

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.288 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1767965

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.4	α = 90
b = 31.5	β = 107.4
c = 54.5	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
REFMAC	phasing
Aimless	data reduction

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., 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.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	CE140100011

Revision History  

• Version 1.0: 2021-03-10
  Type: Initial release
  
• Version 1.1: 2021-05-26
  Changes: Database references
• Version 1.2: 2023-08-16
  Changes: Data collection, Database references
• Version 1.3: 2023-10-18
  Changes: Refinement description