Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Jan 28;95(4):e02019-20.
doi: 10.1128/JVI.02019-20. Print 2021 Jan 28.

Structure of Nonstructural Protein 1 from SARS-CoV-2

Affiliations

Structure of Nonstructural Protein 1 from SARS-CoV-2

Lauren K Clark et al. J Virol. .

Abstract

The periodic emergence of novel coronaviruses (CoVs) represents an ongoing public health concern with significant health and financial burdens worldwide. The most recent occurrence originated in the city of Wuhan, China, where a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) emerged causing severe respiratory illness and pneumonia. The continual emergence of novel coronaviruses underscores the importance of developing effective vaccines as well as novel therapeutic options that target either viral functions or host factors recruited to support coronavirus replication. The CoV nonstructural protein 1 (nsp1) has been shown to promote cellular mRNA degradation, block host cell translation, and inhibit the innate immune response to virus infection. Interestingly, deletion of the nsp1-coding region in infectious clones prevented the virus from productively infecting cultured cells. Because of nsp1's importance in the CoV life cycle, it has been highlighted as a viable target for both antiviral therapy and vaccine development. However, the fundamental molecular and structural mechanisms that underlie nsp1 function remain poorly understood, despite its critical role in the viral life cycle. Here, we report the high-resolution crystal structure of the amino globular portion of SARS-CoV-2 nsp1 (residues 10 to 127) at 1.77-Å resolution. A comparison of our structure with the SARS-CoV-1 nsp1 structure reveals how mutations alter the conformation of flexible loops, inducing the formation of novel secondary structural elements and new surface features. Paired with the recently published structure of the carboxyl end of nsp1 (residues 148 to 180), our results provide the groundwork for future studies focusing on SARS-CoV-2 nsp1 structure and function during the viral life cycle.IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. One protein known to play a critical role in the coronavirus life cycle is nonstructural protein 1 (nsp1). As such, it has been highlighted in numerous studies as a target for both the development of antivirals and the design of live-attenuated vaccines. Here, we report the high-resolution crystal structure of nsp1 derived from SARS-CoV-2 at 1.77-Å resolution. This structure will facilitate future studies focusing on understanding the relationship between structure and function for nsp1. In turn, understanding these structure-function relationships will allow nsp1 to be fully exploited as a target for both antiviral development and vaccine design.

Keywords: COVID-19; SARS-CoV-2; X-ray crystallography; coronavirus; nonstructural protein 1; severe acute respiratory syndrome.

PubMed Disclaimer

Figures

FIG 1
FIG 1
Crystal structure of SARS-CoV-2 nsp1. Ribbon diagram of the SARS-CoV-2 nsp110–126 with the α-helices in blue, β-strands in cyan, and loops in gray. All secondary structural elements are labeled. Coordinates have been deposited under PDB ID 7K7P.
FIG 2
FIG 2
Comparison of the SARS-CoV-2 and SARS-CoV-1 nsp1 structures. (A) Sequence alignment between the nsp1 structures derived from SARS-CoV-2 and SARS-CoV-1 with amino acid differences highlighted in green. (B) Ribbon diagram of the SARS-CoV-2 nsp110–127 with amino acid differences with SARS-CoV-1 nsp112–127. The amino acid position is labeled in black with the sequence identity of SARS-CoV-1 at that position labeled in red and SARS-CoV-2 in light blue. (C) Overlay of the structures of nsp1 derived from SARS-CoV-1 (red) and SARS-CoV-2 (blue). PDB ID 2HSX for SARS-CoV-1 nsp112–127 and 7K7P for SARS-CoV-2 nsp110–127.
FIG 3
FIG 3
Differences in secondary structural elements between SARS-CoV-2 and SARS-CoV-1 nsp1. (A) Ribbon diagram of the stabilization via polar contacts of the 310 helix present in SARS-CoV-2 nsp1 but not in SARS-CoV-1 nsp1. Amino acids specified in the text are indicated in cyan and pink for SARS-CoV-2 and SARS-CoV-1, respectively. (B) Extension of the β4 strand in SARS-CoV-2 (blue) relative to that in SARS-CoV-1 (red). Mutations between the two viruses are labeled with their respective amino acid identity and position. Each mutation is also indicated in cyan for SARS-CoV-2 and pink for SARS-CoV-1. (C) An additional β-strand is present in the SARS-CoV-2 nsp1. Amino acids that compose this segment of both proteins are labeled and indicated in cyan for SARS-CoV-2 and pink for SARS-CoV-1. For all panels, SARS-CoV-2 nsp1 is in blue gray, SARS-CoV-1 nsp1 is in light pink, and polar contacts are indicated by yellow dashed lines.
FIG 4
FIG 4
Conformational differences in major loops between SARS-CoV-2 and SARS-CoV-1 nsp1. Ribbon diagram of SARS-CoV-2 and SARS-CoV-1 nsp1 with the loops located between β3 and β4 (A) and β4 and β6 (B) indicated in blue for SARS-CoV-2 and red for SARS-CoV-1. Residues mutated between the two viruses that are also involved in polar contacts are labeled as well as indicated in cyan for SARS-CoV-2 and pink for SARS-CoV-1. Polar contacts are indicated by yellow dashed lines.
FIG 5
FIG 5
Differences in electrostatic surface potential between SARS-CoV-1 nsp1 and SARS-CoV-2 nsp1. (A to H) Surface models of both proteins with amino acids contributing to the differences in electrostatic character labeled. Secondary structural elements that contribute to differences in surface contours are highlighted in purple for the loop between β3 and β4 and in yellow for β5, found in SARS-CoV-2 but not SARS-CoV-1 nsp1. Residues that are mutated between the two viruses are indicated with an asterisk (*).
FIG 6
FIG 6
Structural homology of β- and α-coronavirus nsp1s. Structures of nsp1s from SARS-CoV-2 (7K7P), porcine transmissible gastroenteritis coronavirus strain Purdue (3ZBD), porcine epidemic diarrhea virus (5XBC), transmissible gastroenteritis virus (6IVC), swine acute diarrhea syndrome coronavirus (6LPA), and feline infectious peritonitis virus (6LP9) are shown structurally aligned (A) and in common orientations (B to G). (B to G) The common core shared with SARS-CoV-2 is shown in pale coloring, with deviations shown in darker shade coloring. (H) Secondary structural elements of SARS-CoV-2 and α-CoV nsp1 with positions indicated.
FIG 7
FIG 7
Structural prediction of full-length SARS-CoV-2 nsp1. Ribbon diagram of full-length SARS-CoV-2 nsp1 modeled using the I-TASSER platform.

Update of

Similar articles

Cited by

References

    1. Drosten C, Preiser W, Gunther S, Schmitz H, Doerr HW. 2003. Severe acute respiratory syndrome: identification of the etiological agent. Trends Mol Med 9:325–327. doi:10.1016/s1471-4914(03)00133-3. - DOI - PMC - PubMed
    1. Ksiazek TG, Erdman D, Goldsmith CS, Zaki SR, Peret T, Emery S, Tong S, Urbani C, Comer JA, Lim W, Rollin PE, Dowell SF, Ling AE, Humphrey CD, Shieh WJ, Guarner J, Paddock CD, Rota P, Fields B, DeRisi J, Yang JY, Cox N, Hughes JM, LeDuc JW, Bellini WJ, Anderson LJ, Group SW, SARS Working Group. 2003. A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med 348:1953–1966. doi:10.1056/NEJMoa030781. - DOI - PubMed
    1. Peiris JS, Yuen KY, Osterhaus AD, Stohr K. 2003. The severe acute respiratory syndrome. N Engl J Med 349:2431–2441. doi:10.1056/NEJMra032498. - DOI - PubMed
    1. Al-Omari A, Rabaan AA, Salih S, Al-Tawfiq JA, Memish ZA. 2019. MERS coronavirus outbreak: implications for emerging viral infections. Diagn Microbiol Infect Dis 93:265–285. doi:10.1016/j.diagmicrobio.2018.10.011. - DOI - PMC - PubMed
    1. Chan JF, Yuan S, Kok KH, To KK, Chu H, Yang J, Xing F, Liu J, Yip CC, Poon RW, Tsoi HW, Lo SK, Chan KH, Poon VK, Chan WM, Ip JD, Cai JP, Cheng VC, Chen H, Hui CK, Yuen KY. 2020. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet 395:514–523. doi:10.1016/S0140-6736(20)30154-9. - DOI - PMC - PubMed

Publication types

Substances

-