High-resolution structure reveals enhanced 14-3-3 binding by a mutant SARS-CoV-2 nucleoprotein variant with improved replicative fitness

High-resolution structure reveals enhanced 14-3-3 binding by a mutant SARS-CoV-2 nucleoprotein variant with improved replicative fitness Full article

Journal

Biochemical and Biophysical Research Communications
ISSN: 0006-291X , E-ISSN: 1090-2104

Output data

Year: 2025, Volume: 767, Article number : 151915, Pages count : DOI: 10.1016/j.bbrc.2025.151915

Authors

Perfilova Kristina V ¹ , Matyuta Ilya O ² , Minyaev Mikhail E ³ , Boyko Konstantin M ¹ , Cooley Richard B ⁴ , Sluchanko Nikolai N ⁵

Affiliations

1	A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
2	A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia; Moscow Center for Advanced Studies, Kulakova Str. 20, 123592, Moscow, Russia.
3	N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia.
4	GCE4All Center, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA.
5	A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia. Electronic address: nikolai.sluchanko@mail.ru.

Replication of many viruses depends on phosphorylation of viral proteins by host protein kinases and subsequent recruitment of host protein partners. The nucleoprotein (N) of SARS-CoV-2 is heavily phosphorylated and recruits human phosphopeptide-binding 14-3-3 proteins early in infection, which is reversed prior to nucleocapsid assembly in new virions. Among the multiple phosphosites of N, which are particularly dense in the serine/arginine-rich interdomain region, phospho-Thr205 is highly relevant for 14-3-3 recruitment by SARS-CoV-2 N. The context of this site is mutated in most SARS-CoV-2 variants of concern. Among mutations that increase infectious virus titers, the S202R mutation (B.1.526 Iota) causes a striking replication boost (∼166-fold), although its molecular consequences have remained unclear. Here, we show that the S202R-mutated N phosphopeptide exhibits a 5-fold higher affinity for human 14-3-3ζ than the Wuhan variant and we rationalize this effect by solving a high-resolution crystal structure of the complex. The structure revealed an enhanced 14-3-3/N interface contributed by the Arg202 side chain that, in contrast to Ser202, formed multiple stabilizing contacts with 14-3-3, including water-mediated H-bonds and guanidinium pi-pi stacking. These findings provide a compelling link between the replicative fitness of SARS-CoV-2 and the N protein's affinity for host 14-3-3 proteins.

Perfilova K.V. , Matyuta I.O. , Minyaev M.E. , Boyko K.M. , Cooley R.B. , Sluchanko N.N.
High-resolution structure reveals enhanced 14-3-3 binding by a mutant SARS-CoV-2 nucleoprotein variant with improved replicative fitness
Biochemical and Biophysical Research Communications. 2025. V.767. 151915 . DOI: 10.1016/j.bbrc.2025.151915 WOS Scopus OpenAlex

≡ Web of science:	WOS:001488084600001
≡ Scopus:	2-s2.0-105004006290
≡ OpenAlex:	W4409912206