Abstract
Interferon-stimulated gene 56 (ISG56) family members play important roles in blocking viral replication and regulating cellular functions, however, their underlying molecular mechanisms are largely unclear. Here, we present the crystal structure of ISG54, an ISG56 family protein with a novel RNA-binding structure. The structure shows that ISG54 monomers have 9 tetratricopeptide repeat-like motifs and associate to form domain-swapped dimers. The C-terminal part folds into a super-helical structure and has an extensively positively-charged nucleotide-binding channel on its inner surface. EMSA results show that ISG54 binds specifically to some RNAs, such as adenylate uridylate (AU)-rich RNAs, with or without 5′ triphosphorylation. Mutagenesis and functional studies show that this RNA-binding ability is important to its antiviral activity. Our results suggest a new mechanism underlying the antiviral activity of this interferon-inducible gene 56 family member.
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18 May 2022
A Correction to this paper has been published: https://doi.org/10.1038/s41422-022-00660-8
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Acknowledgements
We thank our colleagues Drs Hongfei Wang and Lijie Wu for crystal data collection. We thank Yuanyuan Chen and Xiaoxia Yu in core facility center (Institute of Biophysics, CAS) for technical assistance with the ITC, SPR and ultra-centrifugation experiments. We thank colleagues at the Photon factory, KEK (Japan) and SSRF (China) for assistance in the use of the synchrotron resource. We also thank Drs Xiufan Liu and Shunlin Hu (Yangzhou University) for providing the cDNA of ZJ1-NDV. This work was supported by grants to YL from the Ministry of Science and Technology (863 Project 2006AA02A314; 973 Programs 2007CB914303, 2011CB910304 and 2012CB910204) and the National Natural Science Foundation of China (30925011, 31030024 and 31021062).
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( Supplementary information is linked to the online version of the paper on the Cell Research website.)
Supplementary information
Supplementary information, Figure S1
The aggregation state of ISG54. (PDF 198 kb)
Supplementary information, Figure S2
Sequence alignment of ISG56 family proteins. (PDF 262 kb)
Supplementary information, Figure S3
GST-fused ISG54 was incubated with excess poly (IC). (PDF 56 kb)
Supplementary information, Figure S4
A) The B factor distribution of ISG54. (PDF 98 kb)
Supplementary information, Figure S5
In vitro translation assay. (PDF 124 kb)
Supplementary information, Figure S6
Co-immunoprecipitation shows that ISG54 cannot bind to eIF3c. (PDF 68 kb)
Supplementary information, Table S1
Sequences of model RNAs used for ISG54 binding (PDF 16 kb)
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Yang, Z., Liang, H., Zhou, Q. et al. Crystal structure of ISG54 reveals a novel RNA binding structure and potential functional mechanisms. Cell Res 22, 1328–1338 (2012). https://doi.org/10.1038/cr.2012.111
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DOI: https://doi.org/10.1038/cr.2012.111
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