4R0A

Crystal structure of human TLR8 in complex with uridine mononucleoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Toll-like receptor 8 senses degradation products of single-stranded RNA.

Tanji, H.Ohto, U.Shibata, T.Taoka, M.Yamauchi, Y.Isobe, T.Miyake, K.Shimizu, T.

(2015) Nat Struct Mol Biol 22: 109-115

  • DOI: 10.1038/nsmb.2943
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Toll-like receptor 8 (TLR8) recognizes viral or bacterial single-stranded RNA (ssRNA) and activates innate immune systems. TLR8 is activated by uridine- and guanosine-rich ssRNA as well as by certain synthetic chemicals; however, the molecular basis ...

    Toll-like receptor 8 (TLR8) recognizes viral or bacterial single-stranded RNA (ssRNA) and activates innate immune systems. TLR8 is activated by uridine- and guanosine-rich ssRNA as well as by certain synthetic chemicals; however, the molecular basis for ssRNA recognition has remained unknown. In this study, to elucidate the recognition mechanism of ssRNA, we determined the crystal structures of human TLR8 in complex with ssRNA. TLR8 recognized two degradation products of ssRNA—uridine and a short oligonucleotide—at two distinct sites: uridine bound the site on the dimerization interface where small chemical ligands are recognized, whereas short oligonucleotides bound a newly identified site on the concave surface of the TLR8 horseshoe structure. Site-directed mutagenesis revealed that both binding sites were essential for activation of TLR8 by ssRNA. These results demonstrate that TLR8 is a sensor for both uridine and a short oligonucleotide derived from RNA.


    Organizational Affiliation

    1] Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan. [2] Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toll-like receptor 8
A
811Homo sapiensMutation(s): 0 
Gene Names: TLR8UNQ249/PRO286
Find proteins for Q9NR97 (Homo sapiens)
Go to UniProtKB:  Q9NR97
NIH Common Fund Data Resources
PHAROS  Q9NR97
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
URI
Query on URI

Download CCD File 
A
URIDINE
C9 H12 N2 O6
DRTQHJPVMGBUCF-XVFCMESISA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
MAN
Query on MAN

Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
URIKd:  55000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.444α = 90
b = 133.319β = 90
c = 120.039γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references