3WPI

Crystal structure of mouse TLR9 in complex with inhibitory DNA_super


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9

Ohto, U.Shibata, T.Tanji, H.Ishida, H.Krayukhina, E.Uchiyama, S.Miyake, K.Shimizu, T.

(2015) Nature 520: 702-705

  • DOI: 10.1038/nature14138
  • Primary Citation of Related Structures:  
    3WPB, 3WPC, 3WPD, 3WPE, 3WPF, 3WPG, 3WPH, 3WPI

  • PubMed Abstract: 
  • Innate immunity serves as the first line of defence against invading pathogens such as bacteria and viruses. Toll-like receptors (TLRs) are examples of innate immune receptors, which sense specific molecular patterns from pathogens and activate immune responses ...

    Innate immunity serves as the first line of defence against invading pathogens such as bacteria and viruses. Toll-like receptors (TLRs) are examples of innate immune receptors, which sense specific molecular patterns from pathogens and activate immune responses. TLR9 recognizes bacterial and viral DNA containing the cytosine-phosphate-guanine (CpG) dideoxynucleotide motif. The molecular basis by which CpG-containing DNA (CpG-DNA) elicits immunostimulatory activity via TLR9 remains to be elucidated. Here we show the crystal structures of three forms of TLR9: unliganded, bound to agonistic CpG-DNA, and bound to inhibitory DNA (iDNA). Agonistic-CpG-DNA-bound TLR9 formed a symmetric TLR9-CpG-DNA complex with 2:2 stoichiometry, whereas iDNA-bound TLR9 was a monomer. CpG-DNA was recognized by both protomers in the dimer, in particular by the amino-terminal fragment (LRRNT-LRR10) from one protomer and the carboxy-terminal fragment (LRR20-LRR22) from the other. The iDNA, which formed a stem-loop structure suitable for binding by intramolecular base pairing, bound to the concave surface from LRR2-LRR10. This structure serves as an important basis for improving our understanding of the functional mechanisms of TLR9.


    Organizational Affiliation

    1] Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan [2] Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Toll-like receptor 9A803Mus musculusMutation(s): 7 
Gene Names: Tlr9
UniProt
Find proteins for Q9EQU3 (Mus musculus)
Explore Q9EQU3 
Go to UniProtKB:  Q9EQU3
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*TP*CP*AP*AP*TP*AP*GP*GP*GP*TP*GP*AP*GP*GP*GP*G)-3')B18synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    NAG (Subject of Investigation/LOI)
    Query on NAG

    Download Ideal Coordinates CCD File 
    C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
    C8 H15 N O6
    OVRNDRQMDRJTHS-FMDGEEDCSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.25 Å
    • R-Value Free: 0.254 
    • R-Value Work: 0.221 
    • R-Value Observed: 0.223 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 137.33α = 90
    b = 129.72β = 92.17
    c = 71.36γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    MOSFLMdata reduction
    SCALAdata scaling
    MOLREPphasing

    Structure Validation

    View Full Validation Report



    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    • Deposited Date: 2014-01-11 
    • Released Date: 2015-02-11 
    • Deposition Author(s): Ohto, U., Shimizu, T.

    Revision History  (Full details and data files)

    • Version 1.0: 2015-02-11
      Type: Initial release
    • Version 1.1: 2015-05-06
      Changes: Database references
    • Version 1.2: 2020-07-29
      Type: Remediation
      Reason: Carbohydrate remediation
      Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary