9DK8 | pdb_00009dk8

TRIF TIR Filament Cryo-EM Structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for TIR domain-mediated innate immune signaling by Toll-like receptor adaptors TRIF and TRAM.

Manik, M.K.Pan, M.Xiao, L.Gu, W.Kim, H.Pospich, S.Hedger, A.Vajjhala, P.R.Lee, M.Y.L.Qian, X.Landsberg, M.J.Ve, T.Nanson, J.D.Raunser, S.Stacey, K.J.Wu, H.Kobe, B.

(2025) Proc Natl Acad Sci U S A 122: e2418988122-e2418988122

  • DOI: https://doi.org/10.1073/pnas.2418988122
  • Primary Citation of Related Structures:  
    9DK8, 9DKI, 9DLG

  • PubMed Abstract: 

    Innate immunity relies on Toll-like receptors (TLRs) to detect pathogen-associated molecular patterns. The TIR (Toll/interleukin-1 receptor) domain-containing TLR adaptors TRIF (TIR domain-containing adaptor-inducing interferon-β) and TRAM (TRIF-related adaptor molecule) are essential for MyD88-independent TLR signaling. However, the structural basis of TRIF and TRAM TIR domain-based signaling remains unclear. Here, we present cryo-EM structures of filaments formed by TRIF and TRAM TIR domains at resolutions of 3.3 Å and 5.6 Å, respectively. Both structures reveal two-stranded parallel helical arrangements. Functional studies underscore the importance of intrastrand interactions, mediated by the BB-loop, and interstrand interactions in TLR4-mediated signaling. We also report the crystal structure of the monomeric TRAM TIR domain bearing the BB loop mutation C117H, which reveals conformational differences consistent with its inactivity. Our findings suggest a unified signaling mechanism by the TIR domains of the four signaling TLR adaptors MyD88, MAL, TRIF, and TRAM and reveal potential therapeutic targets for immunity-related disorders.


  • Organizational Affiliation
    • Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TIR domain-containing adapter molecule 1545Homo sapiensMutation(s): 0 
Gene Names: TICAM1PRVTIRBTRIF
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IUC6 (Homo sapiens)
Explore Q8IUC6 
Go to UniProtKB:  Q8IUC6
PHAROS:  Q8IUC6
GTEx:  ENSG00000127666 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IUC6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release