4Z0C

Crystal structure of TLR13-ssRNA13 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.191 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural basis for specific recognition of single-stranded RNA by Toll-like receptor 13

Song, W.Wang, J.Han, Z.Zhang, Y.Zhang, H.Wang, W.Chang, J.Xia, B.Fan, S.Zhang, D.Wang, J.Wang, H.W.Chai, J.

(2015) Nat Struct Mol Biol 22: 782-787

  • DOI: 10.1038/nsmb.3080
  • Primary Citation of Related Structures:  
    4Z0C

  • PubMed Abstract: 
  • Toll-like receptors (TLRs) have crucial roles in innate immunity, functioning as pattern-recognition receptors. TLR13 recognizes a conserved sequence from bacterial 23S rRNA and then triggers an immune response. Here we report the crystal structure of the mouse TLR13 ectodomain bound by a 13-nt single-stranded (ss) RNA derived from 23S rRNA ...

    Toll-like receptors (TLRs) have crucial roles in innate immunity, functioning as pattern-recognition receptors. TLR13 recognizes a conserved sequence from bacterial 23S rRNA and then triggers an immune response. Here we report the crystal structure of the mouse TLR13 ectodomain bound by a 13-nt single-stranded (ss) RNA derived from 23S rRNA. The ssRNA induces TLR13 dimerization but assumes a stem-loop-like structure that is completely different from that in the bacterial ribosome but nevertheless is crucial for TLR13 recognition. Most of the RNA nucleotides are splayed out to make base-specific contacts with the concave surface of TLR13, and RNA-specific interactions are important to allow TLR13 to distinguish RNA from DNA. Interestingly, a viral-derived 16-nt ssRNA predicted to form a similar stem-loop-like structure also induces TLR13 activation. Together, our results reveal the structural mechanism of TLR13's sequence- and conformation-specific recognition of ssRNA.


    Organizational Affiliation

    Tsinghua-Peking Center for Life Sciences, Beijing, China.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Toll-like receptor 13 AD709Mus musculusMutation(s): 0 
Gene Names: Tlr13
EC: 3.2.2.6
Find proteins for Q6R5N8 (Mus musculus)
Explore Q6R5N8 
Go to UniProtKB:  Q6R5N8
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-R(P*AP*CP*GP*GP*AP*AP*AP*GP*AP*CP*CP*CP*C)-3')B, C13synthetic construct
    Oligosaccharides

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    Entity ID: 3
    MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
    2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
    E, F, G, H, I, J
    2 N-Glycosylation Oligosaccharides Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.30 Å
    • R-Value Free: 0.244 
    • R-Value Work: 0.191 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 112.549α = 90
    b = 115.209β = 90
    c = 167.611γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data scaling
    PDB_EXTRACTdata extraction
    PHENIXphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2015-10-07
      Type: Initial release
    • Version 1.1: 2015-10-14
      Changes: Derived calculations
    • Version 1.2: 2015-10-28
      Changes: Database references
    • Version 2.0: 2020-07-29
      Type: Remediation
      Reason: Carbohydrate remediation
      Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary