8W8M | pdb_00008w8m

Cryo-EM structure of helical filament of MyD88 TIR

• PDB DOI: https://doi.org/10.2210/pdb8W8M/pdb
• EM Map EMD-37355: EMDB EMDataResource

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


• Deposited: 2023-09-04 Released: 2024-09-04 
• 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: 3.28 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Literature

From Monomers to Oligomers: Structural Mechanism of Receptor-Triggered MyD88 Assembly in Innate Immune Signaling

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

(2024) bioRxiv 

• DOI: https://doi.org/10.1101/2024.09.13.612588

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 102-mer - A102 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,717.86 kDa 
• Atom Count: 113,934 
• Modeled Residue Count: 13,770 
• Deposited Residue Count: 14,688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myeloid differentiation primary response protein MyD88	A [auth D2], AA [auth J1], AB [auth R3], AC [auth 2A], B [auth D3], BA [auth G2], BB [auth P1], BC [auth 3A], C [auth E1], CA [auth G3], CB [auth S2], CC [auth Y1], D [auth E2], DA [auth H1], DB [auth S3], DC [auth 2B], E [auth E3], EA [auth H2], EB [auth T1], EC [auth 3B], F [auth F1], FA [auth H3], FB [auth T2], FC [auth 1C], G [auth F2], GA [auth I1], GB [auth T3], GC [auth 2C], H [auth F3], HA [auth I2], HB [auth U1], HC [auth 3C], I [auth D1], IA [auth I3], IB [auth U2], IC [auth 1D], J [auth A2], JA [auth G1], JB [auth U3], JC [auth 2D], K [auth A3], KA [auth M2], KB [auth S1], KC [auth 3D], L [auth B1], LA [auth M3], LB [auth V2], LC [auth 1B], M [auth B2], MA [auth N1], MB [auth V3], MC [auth ZD], N [auth B3], NA [auth N2], NB [auth W1], NC [auth YE], O [auth C1], OA [auth N3], OB [auth W2], OC [auth ZE], P [auth C2], PA [auth O1], PB [auth W3], PC [auth 1E], Q [auth C3], QA [auth O2], QB [auth X1], QC [auth YF], R [auth A1], RA [auth O3], RB [auth X2], RC [auth ZF], S [auth J2], SA [auth M1], SB [auth X3], SC [auth 1F], T [auth J3], TA [auth P2], TB [auth V1], TC [auth YD], U [auth K1], UA [auth P3], UB [auth Y2], UC [auth 2E], V [auth K2], VA [auth Q1], VB [auth Y3], VC [auth 3E], W [auth K3], WA [auth Q2], WB [auth Z1], WC [auth 2F], X [auth L1], XA [auth Q3], XB [auth Z2], XC [auth 3F], Y [auth L2], YA [auth R1], YB [auth Z3], Z [auth L3], ZA [auth R2], ZB [auth 1A]	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: 3.28 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
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: 2024-09-04
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Structure summary