9DLG | pdb_00009dlg

CryoEM structure of the TIR domain from human TRAM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 2A [auth B],
B [auth A],
C,
D,
E
156Homo sapiensMutation(s): 0 
Gene Names: TICAM2TIRAP3TIRPTRAM
UniProt & NIH Common Fund Data Resources
Find proteins for Q86XR7 (Homo sapiens)
Explore Q86XR7 
Go to UniProtKB:  Q86XR7
PHAROS:  Q86XR7
GTEx:  ENSG00000243414 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86XR7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia2025931
National Health and Medical Research Council (NHMRC, Australia)Australia1196590
Australian Research Council (ARC)AustraliaFL180100109
Australian Research Council (ARC)AustraliaFT200100572
Australian Research Council (ARC)AustraliaDE170100783

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Data collection, Data processing