5GMG | pdb_00005gmg

Crystal structure of monkey TLR7 in complex with loxoribine and polyU

• PDB DOI: https://doi.org/10.2210/pdb5GMG/pdb
• NAKB: 5GMG

• Classification: IMMUNE SYSTEM/RNA
• Organism(s): Macaca mulatta, Homo sapiens
• Expression System: Drosophila
• Mutation(s): Yes 


• Deposited: 2016-07-14 Released: 2016-11-02 
• Deposition Author(s): Zhang, Z., Ohto, U., Shimizu, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.258 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

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

• PubMed: 27742543 
• DOI: https://doi.org/10.1016/j.immuni.2016.09.011
• Primary Citation Related Structures: 
  5GMF, 5GMG, 5GMH


• 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. 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.

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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.
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 Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan.
Department of Chemistry, Graduate School of Science and Technology, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji, Tokyo 192-0397, 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 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.

Macromolecule Content 

• Total Structure Weight: 193.34 kDa 
• Atom Count: 12,680 
• Modeled Residue Count: 1,532 
• Deposited Residue Count: 1,642 
• 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, B	817	Macaca mulatta	Mutation(s): 4  Gene Names: TLR7
UniProt
Find proteins for B3Y653 (Macaca mulatta) Explore B3Y653  Go to UniProtKB:  B3Y653
Glycosylation
Glycosylation Sites: 4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*UP*UP*U)-3')	C, D	4	Homo sapiens

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, 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
SDL	J [auth B], K [auth B]	2-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-7-prop-2-enyl-1~{H}-purine-6,8-dione C13 H17 N5 O6 VDCRFBBZFHHYGT-IOSLPCCCSA-N
NAG	G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	O [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
SDL	BindingDB:  5GMG	EC50: 3.22e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.258 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.277	α = 90
b = 99.41	β = 98.58
c = 112.096	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Zhang, Z., Ohto, U., Shimizu, T.

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection, Database references, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary