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

Nature Structural and Molecular Biology

Volumn 22, Issue 10, 2015, Pages 782-787

  Song, Wen ^a,b   Wang, Jia ^a,b   Han, Zhifu ^a,b   Zhang, Yifan ^c   Zhang, Heqiao ^a   Wang, Weiguang ^a   Chang, Junbiao ^d   Xia, Bingshu ^c   Fan, Shilong ^a,b   Zhang, Dekai ^c   Wang, Jiawei ^a   Wang, Hong Wei ^a,b   Chai, Jijie ^a,b  

^a TSINGHUA UNIVERSITY   (China)

^b Tsinghua University   (China)

^c TEXAS A AND M HEALTH SCIENCE CENTER   (United States)

^d ZHENGZHOU UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEOTIDE; RNA 23S; SINGLE STRANDED RNA; TOLL LIKE RECEPTOR; TOLL LIKE RECEPTOR 13; UNCLASSIFIED DRUG; LUCIFERASE; OLIGONUCLEOTIDE; PROTEIN BINDING; TLR13 PROTEIN, MOUSE;

ARTICLE; CRYSTAL STRUCTURE; DIMERIZATION; HUMAN; HUMAN CELL; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN POLYMERIZATION; PROTEIN RNA BINDING; RIBOSOME; RNA CONFORMATION; RNA STRUCTURE; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; CRYOELECTRON MICROSCOPY; CRYSTALLIZATION; GENETICS; IMAGE PROCESSING; METABOLISM; MOUSE; PROTEIN CONFORMATION; REAL TIME POLYMERASE CHAIN REACTION; SIZE EXCLUSION CHROMATOGRAPHY; TRANSMISSION ELECTRON MICROSCOPY;

ANIMALS; CHROMATOGRAPHY, GEL; CRYOELECTRON MICROSCOPY; CRYSTALLIZATION; DIMERIZATION; IMAGE PROCESSING, COMPUTER-ASSISTED; LUCIFERASES; MICE; MICROSCOPY, ELECTRON, TRANSMISSION; MODELS, MOLECULAR; OLIGONUCLEOTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; REAL-TIME POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 23S; TOLL-LIKE RECEPTORS;

EID: 84943451638     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.3080     Document Type: Article

References (44)

1. Takeuchi, O. &Akira, S. Pattern recognition receptors and inflammation. Cell 140, 805-820 (2010).
2. Aderem, A. &Ulevitch, R.J. Toll-like receptors in the induction of the innate immune response. Nature 406, 782-787 (2000).
3. Kang, J.Y. &Lee, J.O. Structural biology of the Toll-like receptor family. Annu. Rev. Biochem. 80, 917-941 (2011).
4. Botos, I., Segal, D.M. &Davies, D.R. The structural biology of Toll-like receptors. Structure 19, 447-459 (2011).
5. Blasius, A.L. &Beutler, B. Intracellular toll-like receptors. Immunity 32, 305-315 (2010).
6. Alexopoulou, L., Holt, A.C., Medzhitov, R. &Flavell, R.A. Recognition of double-stranded RNA and activation of NF-κB by Toll-like receptor 3. Nature 413, 732-738 (2001).
7. Heil, F. et al. Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8. Science 303, 1526-1529 (2004).
8. Diebold, S.S., Kaisho, T., Hemmi, H., Akira, S. &Reis e Sousa, C. Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA. Science 303, 1529-1531 (2004).
9. Hemmi, H. et al. A Toll-like receptor recognizes bacterial DNA. Nature 408, 740-745 (2000).
10. Oldenburg, M. et al. TLR13 recognizes bacterial 23S rRNA devoid of erythromycin resistance-forming modification. Science 337, 1111-1115 (2012).
11. Li, X.D. &Chen, Z.J. Sequence specific detection of bacterial 23S ribosomal RNA by TLR13. eLife 1, e00102 (2012).
12. Shi, Z. et al. A novel Toll-like receptor that recognizes vesicular stomatitis virus. J. Biol. Chem. 286, 4517-4524 (2011).
13. Jin, M.S. et al. Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide. Cell 130, 1071-1082 (2007).
14. Liu, L. et al. Structural basis of toll-like receptor 3 signaling with double-stranded RNA. Science 320, 379-381 (2008).
15. Park, B.S. et al. The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex. Nature 458, 1191-1195 (2009).
16. Kang, J.Y. et al. Recognition of lipopeptide patterns by Toll-like receptor 2-Toll-like receptor 6 heterodimer. Immunity 31, 873-884 (2009).
17. Yoon, S.I. et al. Structural basis of TLR5-flagellin recognition and signaling. Science 335, 859-864 (2012).
18. Tanji, H., Ohto, U., Shibata, T., Miyake, K. &Shimizu, T. Structural reorganization of the Toll-like receptor 8 dimer induced by agonistic ligands. Science 339, 1426-1429 (2013).
19. Ohto, U. et al. Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9. Nature 520, 702-705 (2015).
20. Dunkle, J.A., Xiong, L., Mankin, A.S. &Cate, J.H. Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action. Proc. Natl. Acad. Sci. USA 107, 17152-17157 (2010).
21. Thapar, R., Denmon, A.P. &Nikonowicz, E.P. Recognition modes of RNA tetraloops and tetraloop-like motifs by RNA-binding proteins. Wiley Interdiscip. Rev. RNA 5, 49-67 (2014).
22. Du, Z. et al. Crystal structure of the first KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.7 A. J. Biol. Chem. 280, 38823-38830 (2005).
23. Weiss, M.S., Brandl, M., Suhnel, J., Pal, D. &Hilgenfeld, R. More hydrogen bonds for the (structural) biologist. Trends Biochem. Sci. 26, 521-523 (2001).
24. Tanji, H. et al. Toll-like receptor 8 senses degradation products of single-stranded RNA. Nat. Struct. Mol. Biol. 22, 109-115 (2015).
25. Otwinowski, Z. &Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
26. Radermacher, M., Wagenknecht, T., Verschoor, A. &Frank, J. Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. J. Microsc. 146, 113-136 (1987).
27. Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38-46 (2007).
28. van Heel, M. &Keegstra, W. IMAGIC: a fast, flexible and friendly image analysis software system. Ultramicroscopy 7, 113-129 (1981).
29. Frank, J. et al. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. J. Struct. Biol. 116, 190-199 (1996).
30. Shaikh, T.R. et al. SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat. Protoc. 3, 1941-1974 (2008).
31. Scheres, S.H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519-530 (2012).
32. Li, X. et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10, 584-590 (2013).
33. Mindell, J.A. &Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol. 142, 334-347 (2003).
34. McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
35. Terwilliger, T.C. Using prime-and-switch phasing to reduce model bias in molecular replacement. Acta Crystallogr. D Biol. Crystallogr. 60, 2144-2149 (2004).
36. Terwilliger, T.C. Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr. D Biol. Crystallogr. 59, 38-44 (2003).
37. Terwilliger, T.C. Automated side-chain model building and sequence assignment by template matching. Acta Crystallogr. D Biol. Crystallogr. 59, 45-49 (2003).
38. Read, R.J. Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Crystallogr. A 42, 140-149 (1986).
39. Cowtan, K. The Buccaneer software for automated model building.1. Tracing protein chains. Acta Crystallogr. D Biol. Crystallogr. 62, 1002-1011 (2006).
40. Emsley, P., Lohkamp, B., Scott, W.G. &Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501 (2010).
41. Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221 (2010).
42. Laskowski, R.A., MacArthur, M.W., Moss, D.S. &Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-291 (1993).
43. Vriend, G. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8, 52-56, 29 (1990).
44. Jerabek-Willemsen, M., Wienken, C.J., Braun, D., Baaske, P. &Duhr, S. Molecular interaction studies using microscale thermophoresis. Assay Drug Dev. Technol. 9, 342-353 (2011).