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Structure of N-terminal domain of ZAP indicates how a zinc-finger protein recognizes complex RNA

Nature Structural & Molecular Biology volume 19, pages 430–435 (2012)Cite this article

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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.

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Figure 1: Overall structure of NZAP225.
Figure 2: Roles of positively charged residues in RNA binding and antiviral activity.
Figure 3: Putative RNA-binding cavities.
Figure 4: Intermolecular interactions of ZAP molecules.
Figure 5: Model of ZAP-RNA interaction.

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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.

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  1. Shoudeng Chen and Yihui Xu: These authors contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

    Shoudeng Chen, Kuo Zhang, Jian Sun & Yingfang Liu

  2. Graduate School of the Chinese Academy of Sciences, Beijing, China

    Shoudeng Chen, Kuo Zhang & Jian Sun

  3. Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

    Yihui Xu, Xinlu Wang & Guangxia Gao

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  1. Shoudeng Chen
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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

Correspondence to Guangxia Gao or Yingfang Liu.

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The authors declare no competing financial interests.

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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

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