5GMF

Crystal structure of monkey TLR7 in complex with guanosine and polyU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Analysis Reveals that Toll-like Receptor 7 Is a Dual Receptor for Guanosine and Single-Stranded RNA

Zhang, Z.Ohto, U.Shibata, T.Krayukhina, E.Taoka, M.Yamauchi, Y.Tanji, H.Isobe, T.Uchiyama, S.Miyake, K.Shimizu, T.

(2016) Immunity 45: 737-748

  • DOI: 10.1016/j.immuni.2016.09.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Toll-like receptor 7 (TLR7) is a single-stranded RNA (ssRNA) sensor in innate immunity and also responds to guanosine and chemical ligands, such as imidazoquinoline compounds. However, TLR7 activation mechanism by these ligands remain largely unknown ...

    Toll-like receptor 7 (TLR7) is a single-stranded RNA (ssRNA) sensor in innate immunity and also responds to guanosine and chemical ligands, such as imidazoquinoline compounds. However, TLR7 activation mechanism by these ligands remain largely unknown. Here, we generated crystal structures of three TLR7 complexes, and found that all formed an activated m-shaped dimer with two ligand-binding sites. The first site conserved in TLR7 and TLR8 was used for small ligand-binding essential for its activation. The second site spatially distinct from that of TLR8 was used for a ssRNA-binding that enhanced the affinity of the first-site ligands. The first site preferentially recognized guanosine and the second site specifically bound to uridine moieties in ssRNA. Our structural, biochemical, and mutagenesis studies indicated that TLR7 is a dual receptor for guanosine and uridine-containing ssRNA. Our findings have important implications for understanding of TLR7 function, as well as for therapeutic manipulation of TLR7 activation.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan; Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.,Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.,Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address: shimizu@mol.f.u-tokyo.ac.jp.,Department of Chemistry, Graduate School of Science and Technology, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji, Tokyo 192-0397, Japan.,Division of Innate Immunity, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toll-like receptor 7
A, B, C, D
817Macaca mulattaMutation(s): 4 
Gene Names: TLR7
Find proteins for B3Y653 (Macaca mulatta)
Go to Gene View: TLR7
Go to UniProtKB:  B3Y653
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*UP*UP*UP*U)-3')E,F,G,H4Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GMP
Query on GMP

Download SDF File 
Download CCD File 
B, C, D
GUANOSINE
C10 H13 N5 O5
NYHBQMYGNKIUIF-UUOKFMHZSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GMPKd: 1000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 98.084α = 93.83
b = 111.335β = 94.34
c = 113.376γ = 91.48
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-11-02
    Type: Initial release