8YYM | pdb_00008yym

Cryo-EM structure of cylindrical fiber of MyD88 TIR

• PDB DOI: https://doi.org/10.2210/pdb8YYM/pdb
• EM Map EMD-39676: EMDB EMDataResource

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


• Deposited: 2024-04-04 Released: 2025-03-26 
• Deposition Author(s): Kasai, K., Imamura, K., Narita, A., Makino, F., Miyata, T., Kato, T., Namba, K., Onishi, H., Tochio, H.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural Mechanism of Receptor-Triggered MyD88 Oligomeric Assembly in Innate Immune Signaling.

Kasai, K., Imamura, K., Uno, M., Nukui, S., Sekiyama, N., Miyata, T., Makino, F., Yamada, R., Takahashi, Y., Kodera, N., Namba, K., Ohnishi, H., Narita, A., Konno, H., Tochio, H.

(2026) Nat Commun 

• PubMed: 41997963 
• DOI: https://doi.org/10.1038/s41467-026-71836-8
• Primary Citation Related Structures: 
  8W8M, 8YYM


• PubMed Abstract: 
  

  MyD88 plays a pivotal role in Toll-like receptor (TLR) and interleukin-1 family signaling through its oligomerization upon receptor activation, leading to downstream protein recruitment. The Toll/interleukin-1 receptor domain of MyD88 (TIR _MyD88 ) is responsible for this receptor-mediated oligomerization, but the detailed mechanism involved remains elusive. Here we investigate the structure of TIR _MyD88 oligomers and their interactions with TLRs. Cryoelectron microscopy reveals that tandemly arrayed TIR _MyD88 subunits form an antiparallel double-stranded filament that can further form rings and cylindrical filaments. Moreover, the self-assembly of TIR _MyD88 in vitro is markedly accelerated by dimeric rather than monomeric receptor TIRs, possibly reflecting the signal initiation step in vivo. High-speed atomic force microscopy further captures the dynamic processes of oligomerization of TIR _MyD88 , in addition to its direct interaction with the receptor TIRs. These results reveal a regulatory mechanism of TIR _MyD88 oligomerization underlying the signal initiation step.

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Organizational Affiliation: 
• Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan.
Graduate School of Frontier Biosciences, The University of Osaka, 1-3 Yamadaoka, Suita, Osaka, Japan.
JEOL YOKOGUSHI Research Alliance Laboratories, The University of Osaka, 1-3 Yamadaoka, Suita, Osaka, Japan.
JEOL Ltd., Akishima, 3-1-2 Musashino, Akishima, Tokyo, Japan.
Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-cho, Kanazawa, Ishikawa, Japan.
WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-cho, Kanazawa, Ishikawa, Japan.
Department of Pediatrics, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, Japan.
Laboratory of Intractable and Rare Diseases, Graduate school of medicine, Gifu University, 1-1 Yanagido, Gifu, Japan.
Center for One Medicine Innovative Translational Research (COMIT), Gifu University, 1-1 Yanagido, Gifu, Japan.
Department of Biological Science, Graduate School of Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan.
Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D26  (Explore in 3D)
Global Stoichiometry: Homo 104-mer - A104 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,751.54 kDa 
• Atom Count: 115,856 
• Modeled Residue Count: 14,040 
• Deposited Residue Count: 14,976 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloid differentiation primary response protein MyD88	A, AA [auth GB], AB [auth N], AC [auth TB], B [auth AA], BA [auth GC], BB [auth NA], BC [auth TC], C [auth AB], CA [auth H], CB [auth NB], CC [auth U], D [auth AC], DA [auth HA], DB [auth NC], DC [auth UA], E [auth B], EA [auth HB], EB [auth O], EC [auth UB], F [auth BA], FA [auth HC], FB [auth OA], FC [auth UC], G [auth BB], GA [auth I], GB [auth OB], GC [auth V], H [auth BC], HA [auth IA], HB [auth OC], HC [auth VA], I [auth C], IA [auth IB], IB [auth P], IC [auth VB], J [auth CA], JA [auth IC], JB [auth PA], JC [auth VC], K [auth CB], KA [auth J], KB [auth PB], KC [auth W], L [auth CC], LA [auth JA], LB [auth PC], LC [auth WA], M [auth D], MA [auth JB], MB [auth Q], MC [auth WB], N [auth DA], NA [auth JC], NB [auth QA], NC [auth WC], O [auth DB], OA [auth K], OB [auth QB], OC [auth X], P [auth DC], PA [auth KA], PB [auth QC], PC [auth XA], Q [auth E], QA [auth KB], QB [auth R], QC [auth XB], R [auth EA], RA [auth KC], RB [auth RA], RC [auth XC], S [auth EB], SA [auth L], SB [auth RB], SC [auth Y], T [auth EC], TA [auth LA], TB [auth RC], TC [auth YA], U [auth F], UA [auth LB], UB [auth S], UC [auth YB], V [auth FA], VA [auth LC], VB [auth SA], VC [auth YC], W [auth FB], WA [auth M], WB [auth SB], WC [auth Z], X [auth FC], XA [auth MA], XB [auth SC], XC [auth ZA], Y [auth G], YA [auth MB], YB [auth T], YC [auth ZB], Z [auth GA], ZA [auth MC], ZB [auth TA], ZC	144	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: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Kasai, K., Imamura, K., Narita, A., Makino, F., Miyata, T., Kato, T., Namba, K., Onishi, H., Tochio, H.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR1762
Japan Society for the Promotion of Science (JSPS)	Japan	16H04752

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release
  
• Version 1.1: 2026-05-06
  Changes: Data collection, Database references