Abstract
Zinc-finger antiviral protein (ZAP) is a host factor that specifically inhibits the replication of certain viruses, such as HIV-1, by targeting viral mRNA for degradation. How ZAP recognizes its target RNA has been unclear. Here we report the crystal structure of the N-terminal domain of rat ZAP (NZAP225), the major functional domain. The overall structure of NZAP225 resembles a tractor, with four zinc-finger motifs located at the bottom. Structural and functional analyses identified multiple positively charged residues and two putative RNA-binding cavities forming a large putative RNA-binding cleft. ZAP molecules interact to form a dimer that binds to a ZAP-responsive RNA molecule containing two ZAP-binding modules. These results provide insights into how ZAP binds specifically to complex target RNA.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Zhu, Y. et al. Zinc-finger antiviral protein inhibits HIV-1 infection by selectively targeting multiply spliced viral mRNAs for degradation. Proc. Natl. Acad. Sci. USA 108, 15834–15839 (2011).
Müller, S. et al. Inhibition of filovirus replication by the zinc-finger antiviral protein. J. Virol. 81, 2391–2400 (2007).
Bick, M.J. et al. Expression of the zinc-finger antiviral protein inhibits alphavirus replication. J. Virol. 77, 11555–11562 (2003).
Guo, X., Carroll, J.W., Macdonald, M.R., Goff, S.P. & Gao, G. The zinc-finger antiviral protein directly binds to specific viral mRNAs through the CCCH zinc-finger motifs. J. Virol. 78, 12781–12787 (2004).
Zhu, Y. & Gao, G. ZAP-mediated mRNA degradation. RNA Biol. 5, 65–67 (2008).
Chen, G., Guo, X., Lv, F., Xu, Y. & Gao, G. p72 DEAD box RNA helicase is required for optimal function of the zinc-finger antiviral protein. Proc. Natl. Acad. Sci. USA 105, 4352–4357 (2008).
Gao, G., Guo, X. & Goff, S.P. Inhibition of retroviral RNA production by ZAP, a CCCH-type zinc-finger protein. Science 297, 1703–1706 (2002).
Hayakawa, S. et al. ZAPS is a potent stimulator of signaling mediated by the RNA helicase RIG-I during antiviral responses. Nat. Immunol. 12, 37–44 (2011).
Teplova, M. & Patel, D.J. Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1. Nat. Struct. Mol. Biol. 15, 1343–1351 (2008).
Guo, X., Ma, J., Sun, J. & Gao, G. The zinc-finger antiviral protein recruits the RNA processing exosome to degrade the target mRNA. Proc. Natl. Acad. Sci. USA 104, 151–156 (2007).
Law, L.M. et al. Identification of a dominant negative inhibitor of human zinc-finger antiviral protein reveals a functional endogenous pool and critical homotypic interactions. J. Virol. 84, 4504–4512 (2010).
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).
Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
Vagin, A.A. et al. REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr. D Biol. Crystallogr. 60, 2184–2195 (2004).
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).
Collaborative Computational Project. N., The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).
Acknowledgements
We thank K. Ye for advice and valuable discussions, L. Wu, H. Liang, H. Wang and X. Tao for technical assistance, and J. Fleming for critical reading of this manuscript. We thank colleagues at the High Energy Accelerator Research Organization (KEK), Japan, and at the Shanghai Synchrotron Radiation Facility for assistance in the use of the synchrotron resource. This work was supported by grants to Y.L. from the Ministry of Science and Technology (863 Project 2006AA02A314; 973 Programs 2007CB914303, 2012CB910204 and 2011CB910304) and the National Science Foundation (30925011, 31021062 and 31030024) of China, and by grants to G.G. from the National Science Foundation (81030030), the Ministry of Science and Technology (973 Program 2012CB910203) and the Ministry of Health (2012ZX10001-006) of China.
Author information
Authors and Affiliations
Contributions
S.C. and K.Z. obtained the crystal of NZAP; S.C. and J.S. determined the structure; Y.X., X.W. and S.C. carried out the biochemistry and functional experiments, and S.C., Y.X., G.G. and Y.L. wrote this paper.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–6 (PDF 521 kb)
Rights and permissions
About this article
Cite this article
Chen, S., Xu, Y., Zhang, K. et al. Structure of N-terminal domain of ZAP indicates how a zinc-finger protein recognizes complex RNA. Nat Struct Mol Biol 19, 430–435 (2012). https://doi.org/10.1038/nsmb.2243
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nsmb.2243
This article is cited by
-
ZNF283, a Krüppel-associated box zinc finger protein, inhibits RNA synthesis of porcine reproductive and respiratory syndrome virus by interacting with Nsp9 and Nsp10
Veterinary Research (2024)
-
The DNA glycosylase NEIL2 is protective during SARS-CoV-2 infection
Nature Communications (2023)
-
Rational attenuation of RNA viruses with zinc finger antiviral protein
Nature Microbiology (2022)
-
Zinc-finger antiviral protein acts as a tumor suppressor in colorectal cancer
Oncogene (2020)
-
RNA-binding protein isoforms ZAP-S and ZAP-L have distinct antiviral and immune resolution functions
Nature Immunology (2019)