5ZSM | pdb_00005zsm

Crystal structure of monkey TLR7 in complex with GGUCCC

• PDB DOI: https://doi.org/10.2210/pdb5ZSM/pdb
• NAKB: 5ZSM

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


• Deposited: 2018-04-28 Released: 2019-01-30 
• Deposition Author(s): Zhang, Z., Ohto, U., Shimizu, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.273 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Structural Analyses of Toll-like Receptor 7 Reveal Detailed RNA Sequence Specificity and Recognition Mechanism of Agonistic Ligands.

Zhang, Z., Ohto, U., Shibata, T., Taoka, M., Yamauchi, Y., Sato, R., Shukla, N.M., David, S.A., Isobe, T., Miyake, K., Shimizu, T.

(2018) Cell Rep 25: 3371-3381.e5

• PubMed: 30566863 
• DOI: https://doi.org/10.1016/j.celrep.2018.11.081
• Primary Citation Related Structures: 
  5ZSA, 5ZSB, 5ZSC, 5ZSD, 5ZSE, 5ZSF, 5ZSG, 5ZSH, 5ZSI, 5ZSJ, 5ZSL, 5ZSM, 5ZSN, 6IF5


• PubMed Abstract: 
  

  Toll-like receptor 7 (TLR7) is an innate immune receptor for single-stranded RNA (ssRNA) and has important roles in infectious diseases. We previously reported that TLR7 shows synergistic activation in response to two ligands, guanosine and ssRNA. However, the specific ssRNA sequence preference, detailed recognition mode of TLR7 and its ligand, and molecular determinants of TLR7 and TLR8 selectivity remain unknown. Here, we report on TLR7 from a large-scale crystallographic study combined with a multifaceted approach. We reveal that successive uridine-containing ssRNAs fully or moderately bind TLR7, whereas single uridine-containing ssRNAs have reduced affinities. We also reveal the detailed relationships between the chemical structures of ligands and their binding to TLR7. We demonstrate that an engineered TLR8 mutant alters its responsiveness to TLR7-specific ligands. Finally, we identify guanosine 2',3'-cyclic phosphate (2',3'-cGMP) as a possible endogenous ligand for TLR7 with greater affinity than guanosine. The abundant structural information will facilitate future development of treatments targeting TLR7.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address: [e-mail].
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.
Department of Chemistry, Graduate School of Science and Technology, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji, Tokyo 192-0397, Japan.
Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, 2-132 CCRB, 2231 6th Street SE, Minneapolis, MN 55455, USA.
Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Electronic address: [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: 198.51 kDa 
• Atom Count: 13,150 
• Modeled Residue Count: 1,560 
• Deposited Residue Count: 1,658 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 7	A [auth B], B [auth A]	823	Macaca mulatta	Mutation(s): 4  Gene Names: TLR7
UniProt
Find proteins for B3Y653 (Macaca mulatta) Explore B3Y653  Go to UniProtKB:  B3Y653
Glycosylation
Glycosylation Sites: 9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*UP*CP*CP*C)-3')	C [auth D], D [auth E]	6	synthetic construct

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C], F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9K9	DA [auth A], R [auth B]	2-amino-9-[(2S,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-3,9-dihydro-6H-purin-6-one C10 H12 N5 O7 P UASRYODFRYWBRC-UUOKFMHZSA-N
NAG	G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	AA [auth A], BA [auth A], CA [auth A], O [auth B], P [auth B], Q [auth B], X [auth A], Y [auth A], Z [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.273 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.655	α = 90
b = 139.173	β = 90
c = 150.794	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Zhang, Z., Ohto, U., Shimizu, T.

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-03-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary