4R09 | pdb_00004r09

Crystal structure of human TLR8 in complex with ORN06S

• PDB DOI: https://doi.org/10.2210/pdb4R09/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2014-07-30 Released: 2015-01-14 
• Deposition Author(s): Tanji, H., Ohto, U., Shimizu, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.285 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Toll-like receptor 8 senses degradation products of single-stranded RNA.

Tanji, H., Ohto, U., Shibata, T., Taoka, M., Yamauchi, Y., Isobe, T., Miyake, K., Shimizu, T.

(2015) Nat Struct Mol Biol 22: 109-115

• PubMed: 25599397 
• DOI: https://doi.org/10.1038/nsmb.2943
• Primary Citation Related Structures: 
  4R07, 4R08, 4R09, 4R0A


• PubMed Abstract: 
  

  Toll-like receptor 8 (TLR8) recognizes viral or bacterial single-stranded RNA (ssRNA) and activates innate immune systems. TLR8 is activated by uridine- and guanosine-rich ssRNA as well as by certain synthetic chemicals; however, the molecular basis for ssRNA recognition has remained unknown. In this study, to elucidate the recognition mechanism of ssRNA, we determined the crystal structures of human TLR8 in complex with ssRNA. TLR8 recognized two degradation products of ssRNA—uridine and a short oligonucleotide—at two distinct sites: uridine bound the site on the dimerization interface where small chemical ligands are recognized, whereas short oligonucleotides bound a newly identified site on the concave surface of the TLR8 horseshoe structure. Site-directed mutagenesis revealed that both binding sites were essential for activation of TLR8 by ssRNA. These results demonstrate that TLR8 is a sensor for both uridine and a short oligonucleotide derived from RNA.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan.
1] Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan. [2] Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan.
Department of Chemistry, Graduate School of Science and Technology, Tokyo Metropolitan University, Tokyo, Japan.
1] Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan. [2] Department of Chemistry, Graduate School of Science and Technology, Tokyo Metropolitan University, Tokyo, Japan.
Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
1] Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan. [2] Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo, Japan.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 383.59 kDa 
• Atom Count: 24,895 
• Modeled Residue Count: 2,993 
• Deposited Residue Count: 3,244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 8	A, B, C, D	811	Homo sapiens	Mutation(s): 0  Gene Names: TLR8, UNQ249/PRO286
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR97 (Homo sapiens) Explore Q9NR97  Go to UniProtKB:  Q9NR97
PHAROS:  Q9NR97 GTEx:  ENSG00000101916
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: Q9NR97-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, K	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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	F, G, I, J, M, O	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, L, N	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
06S	BA [auth D], Q [auth A], U [auth B], X [auth C]	O-[(2R,3S,4R,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-2-({[(S)-({(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-[(thiophosphonooxy)methyl]tetrahydrofuran-3-yl}oxy)(sulfanyl)phosphoryl]oxy}methyl)-4-hydroxytetrahydrofuran-3-yl] dihydrogen (S)-phosphorothioate C19 H26 N7 O16 P3 S3 PRHQISJBVGJFKN-VXGQQCRQSA-N
UPT	CA [auth D], R [auth A], V [auth B], Y [auth C]	1-[(2R,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-sulfidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4(1H,3H)-dione C9 H11 N2 O7 P S OIDQHQCLWHMGIL-VQAIERIMSA-N
URI	AA [auth D], P [auth A], T [auth B], Z [auth D]	URIDINE C9 H12 N2 O6 DRTQHJPVMGBUCF-XVFCMESISA-N
NAG	DA [auth D], S [auth A], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.285 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.683	α = 90
b = 141.342	β = 89.46
c = 170.042	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Tanji, H., Ohto, U., Shimizu, T.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2015-02-18
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary