5ZLN

Crystal structure of mouse TLR9 in complex with two DNAs (CpG DNA and TCGCCA DNA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

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Literature

Structural basis for species-specific activation of mouse Toll-like receptor 9

Ishida, H.Ohto, U.Shibata, T.Miyake, K.Shimizu, T.

(2018) FEBS Lett 592: 2636-2646

  • DOI: 10.1002/1873-3468.13176
  • Primary Citation of Related Structures:  
    5ZLN

  • PubMed Abstract: 
  • Single-stranded DNA containing unmethylated cytosine-phosphate-guanine (CpG) motifs derived from microorganisms are recognized by Toll-like receptor (TLR) 9 and activate an innate immune response. TLR9 has two DNA-binding sites for CpG DNA and DNA contai ...

    Single-stranded DNA containing unmethylated cytosine-phosphate-guanine (CpG) motifs derived from microorganisms are recognized by Toll-like receptor (TLR) 9 and activate an innate immune response. TLR9 has two DNA-binding sites for CpG DNA and DNA containing cytosine at the second position from the 5'-end; both are required for efficient TLR9 activation in most vertebrate species. However, mouse TLR9 can be dimerized by CpG DNA only, although the underlying mechanism remains elusive. Here, we report the crystal structure of mouse TLR9 complexed with both DNAs. Although most TLR9-CpG DNA interactions are conserved among species, some are unique to mice and involved in species-specificity. These findings provide the structural basis for how mouse TLR9 dimerizes efficiently in response to CpG DNA to activate innate immunity.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Japan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Toll-like receptor 9 AB793Mus musculusMutation(s): 8 
Gene Names: Tlr9
Find proteins for Q9EQU3 (Mus musculus)
Explore Q9EQU3 
Go to UniProtKB:  Q9EQU3
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3')C, D10synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*CP*GP*C)-3')E, F6synthetic construct
      Oligosaccharides

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      Entity ID: 4
      MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
      beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
      G, H
      3 N-Glycosylation Oligosaccharides Interaction
      Entity ID: 5
      MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
      2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
      I, J, K, L, M, N, O, P, Q
      2 N-Glycosylation Oligosaccharides Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.30 Å
      • R-Value Free: 0.238 
      • R-Value Work: 0.191 
      • R-Value Observed: 0.194 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 114.306α = 90
      b = 128.141β = 90
      c = 156.798γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      XDSdata reduction
      Aimlessdata scaling
      MOLREPphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2018-04-25
        Type: Initial release
      • Version 1.1: 2018-08-08
        Changes: Data collection, Database references
      • Version 1.2: 2018-09-12
        Changes: Data collection, Database references
      • Version 2.0: 2020-07-29
        Type: Remediation
        Reason: Carbohydrate remediation
        Changes: Atomic model, Data collection, Derived calculations, Structure summary