6LW1

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

• PDB DOI: https://doi.org/10.2210/pdb6LW1/pdb
• EM Map EMD-30002: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Macaca mulatta
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2020-02-06 Released: 2020-11-11 
• Deposition Author(s): Zhang, Z., Ohto, U., Shimizu, T.

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Experimental Data Snapshot

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

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

• PubMed: 33060576 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 190.47 kDa 
• Atom Count: 12,412 
• Modelled Residue Count: 1,526 
• Deposited Residue Count: 1,646 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 7	A, B	823	Macaca mulatta	Mutation(s): 10  Gene Names: TLR7
UniProt
Find proteins for B3Y653 (Macaca mulatta) Explore B3Y653  Go to UniProtKB:  B3Y653

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EX3 (Subject of Investigation/LOI)	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:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-11 
Deposition Author(s): Zhang, Z., Ohto, U., Shimizu, T.

Revision History  

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