6LVX | pdb_00006lvx

Crystal structure of TLR7/Cpd-1 (SM-374527) complex

• PDB DOI: https://doi.org/10.2210/pdb6LVX/pdb

• 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: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 
  0.252 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

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 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].
Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Sumitomo Dainippon Pharma Co., Ltd., 3-1-98 Kasugade-naka, Konohana-ku, Osaka, 554-0022, Japan.
Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Department of Cell Biology and Anatomy, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, 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.
Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. [e-mail].
Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 193.55 kDa 
• Atom Count: 12,774 
• Modeled Residue Count: 1,542 
• 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
Glycosylation
Glycosylation Sites: 5

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EWL (Subject of Investigation/LOI)	D [auth A], P [auth B]	6-azanyl-2-butoxy-9-(phenylmethyl)-7H-purin-8-one C16 H19 N5 O2 HEKGNUXGYUZNHH-UHFFFAOYSA-N
NAG	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], S [auth B], T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	L [auth A], M [auth A], N [auth A], O [auth A], U [auth B], V [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
EWL	BindingDB:  6LVX	EC50: 63.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free:  0.252 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.754	α = 90
b = 138.504	β = 90
c = 148.462	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

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: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary