PDBsum entry 4z0c

Immune system

PDB id: 4z0c

Contents

Protein chains

709 a.a.

DNA/RNA

Ligands

NAG-NAG ×6

NAG ×20

Waters ×361

PDB id:

4z0c

Name:

Immune system

Title:

Crystal structure of tlr13-ssrna13 complex

Structure:

Toll-like receptor 13. Chain: a, d. Fragment: unp residues 69-777. Engineered: yes. DNA (5'-r(p Ap Cp Gp Gp Ap Ap Ap Gp Ap Cp Cp Cp C)-3'). Chain: b, c. Engineered: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: tlr13. Expressed in: insect cell expression vector ptie1. Expression_system_taxid: 266783. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

Resolution:

2.30Å R-factor: 0.191 R-free: 0.244

Authors:

W.Song,Z.Han,J.Chai

Key ref:

W.Song et al. (2015). Structural basis for specific recognition of single-stranded RNA by Toll-like receptor 13. Nat Struct Biol, 22, 782-787. PubMed id: 26323037 DOI: 10.1038/nsmb.3080

Date:

26-Mar-15 Release date: 07-Oct-15

Protein chains

Q6R5N8  (TLR13_MOUSE) -  Toll-like receptor 13 from Mus musculus

Seq: 991 a.a.

Struc: 709 a.a.

DNA/RNA chains

A-C-G-G-A-A-A-G-A-C-C-C-C 13 bases

A-C-G-G-A-A-A-G-A-C-C-C-C 13 bases

Enzyme reactions

• Enzyme class: E.C.3.2.2.6 - ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase.
• Reaction: NAD⁺ + H2O = ADP-D-ribose + nicotinamide + H⁺

NAD(+) + H2O = ADP-D-ribose + nicotinamide + H(+) (Bound ligand (Het Group name = NAG) matches with 43.75% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nsmb.3080

Nat Struct Biol 22:782-787 (2015)

PubMed id: 26323037

Structural basis for specific recognition of single-stranded RNA by Toll-like receptor 13.

W.Song, J.Wang, Z.Han, Y.Zhang, H.Zhang, W.Wang, J.Chang, B.Xia, S.Fan, D.Zhang, J.Wang, H.W.Wang, J.Chai.

ABSTRACT

Toll-like receptors (TLRs) have crucial roles in innate immunity, functioning as pattern-recognition receptors. TLR13 recognizes a conserved sequence from bacterial 23S rRNA and then triggers an immune response. Here we report the crystal structure of the mouse TLR13 ectodomain bound by a 13-nt single-stranded (ss) RNA derived from 23S rRNA. The ssRNA induces TLR13 dimerization but assumes a stem-loop-like structure that is completely different from that in the bacterial ribosome but nevertheless is crucial for TLR13 recognition. Most of the RNA nucleotides are splayed out to make base-specific contacts with the concave surface of TLR13, and RNA-specific interactions are important to allow TLR13 to distinguish RNA from DNA. Interestingly, a viral-derived 16-nt ssRNA predicted to form a similar stem-loop-like structure also induces TLR13 activation. Together, our results reveal the structural mechanism of TLR13's sequence- and conformation-specific recognition of ssRNA.