Crystal structure of the TIR domain of human myeloid differentiation primary response protein 88.

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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Molecular mechanisms for the subversion of MyD88 signaling by TcpC from virulent uropathogenic Escherichia coli.

Snyder, G.A.Cirl, C.Jiang, J.Chen, K.Waldhuber, A.Smith, P.Rommler, F.Snyder, N.Fresquez, T.Durr, S.Tjandra, N.Miethke, T.Xiao, T.S.

(2013) Proc Natl Acad Sci U S A 110: 6985-6990

  • DOI: https://doi.org/10.1073/pnas.1215770110
  • Primary Citation of Related Structures:  
    4DOM, 4EO7

  • PubMed Abstract: 

    The Toll/IL-1 receptor (TIR) domains are crucial signaling modules during innate immune responses involving the Toll-like receptors (TLRs) and IL-1 receptor (IL-1R). Myeloid differential factor 88 (MyD88) is a central TIR domain-containing adapter molecule responsible for nearly all TLR-mediated signaling and is targeted by a TIR domain-containing protein C (TcpC) from virulent uropathogenic Escherichia coli, a common human pathogen. The mechanism of such molecular antagonism has remained elusive. We present the crystal structure of the MyD88 TIR domain with distinct loop conformations that underscore the functional specialization of the adapter, receptor, and microbial TIR domains. Our structural analyses shed light on the genetic mutations at these loops as well as the Poc site. We demonstrate that TcpC directly associates with MyD88 and TLR4 through its predicted DD and BB loops to impair the TLR-induced cytokine induction. Furthermore, NMR titration experiments identify the unique CD, DE, and EE loops from MyD88 at the TcpC-interacting surface, suggesting that TcpC specifically engages these MyD88 structural elements for immune suppression. These findings thus provide a molecular basis for the subversion of TLR signaling by the uropathogenic E. coli virulence factor TcpC and furnish a framework for the design of novel therapeutic agents that modulate immune activation.

  • Organizational Affiliation

    Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myeloid differentiation primary response protein MyD88144Homo sapiensMutation(s): 0 
Gene Names: MYD88
UniProt & NIH Common Fund Data Resources
Find proteins for Q99836 (Homo sapiens)
Explore Q99836 
Go to UniProtKB:  Q99836
GTEx:  ENSG00000172936 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99836
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MG

Download Ideal Coordinates CCD File 
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CSO
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.876α = 90
b = 56.81β = 90
c = 66.664γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-04-24
    Changes: Database references
  • Version 1.2: 2013-05-08
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-12-06
    Changes: Data collection