6LW1

Cryo-EM structure of TLR7/Cpd-7 (DSR-139970) complex in open form


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural analysis reveals TLR7 dynamics underlying antagonism.

Tojo, S.Zhang, Z.Matsui, H.Tahara, M.Ikeguchi, M.Kochi, M.Kamada, M.Shigematsu, H.Tsutsumi, A.Adachi, N.Shibata, T.Yamamoto, M.Kikkawa, M.Senda, T.Isobe, Y.Ohto, U.Shimizu, T.

(2020) Nat Commun 11: 5204-5204

  • DOI: https://doi.org/10.1038/s41467-020-19025-z
  • Primary Citation of Related Structures:  
    6LVX, 6LVY, 6LVZ, 6LW0, 6LW1

  • PubMed Abstract: 

    Toll-like receptor 7 (TLR7) recognizes both microbial and endogenous RNAs and nucleosides. Aberrant activation of TLR7 has been implicated in several autoimmune diseases including systemic lupus erythematosus (SLE). Here, by modifying potent TLR7 agonists, we develop a series of TLR7-specific antagonists as promising therapeutic agents for SLE. These compounds protect mice against lethal autoimmunity. Combining crystallography and cryo-electron microscopy, we identify the open conformation of the receptor and reveal the structural equilibrium between open and closed conformations that underlies TLR7 antagonism, as well as the detailed mechanism by which TLR7-specific antagonists bind to their binding pocket in TLR7. Our work provides small-molecule TLR7-specific antagonists and suggests the TLR7-targeting strategy for treating autoimmune diseases.


  • Organizational Affiliation

    Sumitomo Dainippon Pharma Co., Ltd., 3-1-98 Kasugade-naka, Konohana-ku, Osaka, 554-0022, Japan. [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toll-like receptor 7
A, B
823Macaca mulattaMutation(s): 10 
Gene Names: TLR7
UniProt
Find proteins for B3Y653 (Macaca mulatta)
Explore B3Y653 
Go to UniProtKB:  B3Y653
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3Y653
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EX3 (Subject of Investigation/LOI)
Query on EX3

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
2-ethoxy-8-(5-fluoranylpyridin-3-yl)-6-methyl-9-[[4-[[(1S,4S)-5-methyl-2,5-diazabicyclo[2.2.1]heptan-2-yl]methyl]phenyl]methyl]purine
C27 H30 F N7 O
RIJUCCOLHSAZPO-GOTSBHOMSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary