SARS-CoV-2 proteins

Unless otherwise stated all data on this page refer to the human proteins. Gene information is provided for human (Hs), mouse (Mm) and rat (Rn).

Overview

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Coronaviruses

Coronaviruses are large, often spherical, enveloped, single-stranded positive-sense RNA viruses, ranging in size from 80-220 nm. Of the four structural proteins encoded in the viral genome, the RNA winds around the highly basic nucleocapsid (N) protein. The three other structural proteins, envelope (E), membrane (M) and spike (S), are transmembrane proteins. The E protein is a small (9-12 kDa) single transmembrane domain protein, which enables virus assembly with the M protein, a larger (23-35 kDa) 3TM protein. Coronaviruses are named for the crown-shaped appearance of the virus due to the large (120+ kDa) S spike 1TM glycoprotein, which forms extended homotrimers. The spike protein binds to the animal host cell by interacting with specific anchoring proteins, typically proteinases, such as angiotensin-converting enzyme 2 or aminopeptidase N. This binding facilitates viral entry into the cell and the release of the genome. Aside from the four structural proteins, the remainder of the genome encodes accessory or non-structural proteins and includes proteinases to cleave the two encoded polyproteins. The remainder of the genome encodes elements for viral replication, assembly and release, as well as proteins which manipulate the host's innate immune system.

Targets

SARS-CoV-2 Envelope protein Show summary »« Hide summary More detailed page

Target Id	3116
Nomenclature	SARS-CoV-2 Envelope protein
Previous and unofficial names	envelope small membrane protein \| orf4
UniProtKB AC	P0DTC4 (CoV2)
Comment	By similarity to other coronavirus E proteins, SARS-CoV-2 E is predicted to constitute a single transmembrane (potentially homopentameric) ion channel with selectivity for monovalent cations over monovalent anions [5,10,13,15].

SARS-CoV-2 Main protease Show summary »« Hide summary More detailed page

Target Id	3111
Nomenclature	SARS-CoV-2 Main protease
Previous and unofficial names	3c-like proteinase \| SARS-CoV-2 M^pro \| Chain A, 3c-like Proteinase \| 3CL protease \| M^pro \| nsp5
Comment	The M^pro protease (also known as nsp5 or 3CL protease) cleaves the two polyproteins encoded by the SARS-CoV-2 genome (pp1a and pp1ab) into a range of non-structural proteins (nsp1-11 from pp1a; nsp1-16 from pp1ab). As these component proteins play crucial roles in viral replication, M^pro is considered to be a strong molecular target for drug development. Small molecule M^pro inhibitors would be predicted to reduce viral replication [3,7].

SARS-CoV-2 Membrane glycoprotein Show summary »« Hide summary More detailed page

Target Id	3117
Nomenclature	SARS-CoV-2 Membrane glycoprotein
Previous and unofficial names	membrane protein
UniProtKB AC	P0DTC5 (CoV2)
Comment	The membrane glycoprotein (M) is usually regarded as the most abundant protein in the coronavirus envelope. By similarity with other coronavirus M proteins it is predicted to be essential for initiating assembly of the viral envelope components [8].

SARS-CoV-2 Non-structural protein 6 Show summary »« Hide summary More detailed page

Target Id	3118
Nomenclature	SARS-CoV-2 Non-structural protein 6
Previous and unofficial names	nsp6
UniProtKB AC	P0DTC6 (CoV2)
Comment	Coronavirus nsp6 proteins limit autophagosome expansion [1]. This mechanism may favour coronavirus infection by damaging autophagosome-mediated delivery of viral components to lysosomes for degradation.

SARS-CoV-2 Non-structural protein 8 Show summary »« Hide summary More detailed page

Target Id	3120
Nomenclature	SARS-CoV-2 Non-structural protein 8
Previous and unofficial names	nsp8
UniProtKB AC	P0DTC8 (CoV2)
Comment	Coronavirus nsp8 proteins form a hexadecameric complex with nsp7 proteins (8 subunits of each) [4,12]. This complex may participate in viral replication by acting as a primase for de novo initiation of RNA synthesis.

SARS-CoV-2 Nucleoprotein Show summary »« Hide summary More detailed page

Target Id	3121
Nomenclature	SARS-CoV-2 Nucleoprotein
Previous and unofficial names	nucleocapsid phosphoprotein
UniProtKB AC	P0DTC9 (CoV2)
Comment	The coronavirus nucleocapsid phosphoprotein (N, or nucleoprotein) is highly basic and binds the viral RNA as a dimeric entity [2] into nucleocapsids which protect the viral genome, while also providing access for replication when required.

SARS-CoV-2 Protein 3a Show summary »« Hide summary More detailed page

Target Id	3115
Nomenclature	SARS-CoV-2 Protein 3a
Previous and unofficial names	orf3a
UniProtKB AC	P0DTC3 (CoV2)
Comment	Protein 3a is a transmembrane pore-forming viral protein (viroporin) with potassium ion channel activity.

SARS-CoV-2 Protein 7a Show summary »« Hide summary More detailed page

Target Id	3119
Nomenclature	SARS-CoV-2 Protein 7a
Previous and unofficial names	orf7a
UniProtKB AC	P0DTC7 (CoV2)
Comment	The main function of the SARS-CoV protein 7a appears to be disruption of host the cell cycle and induction of caspase-dependent apoptosis [11]. By homology SARS-CoV-2 protein 7a is likely to produce the same effect.

SARS-CoV-2 Protein 9b Show summary »« Hide summary More detailed page

Target Id	3122
Nomenclature	SARS-CoV-2 Protein 9b
Previous and unofficial names	orf9b \| Accessory protein 9b \| ORF-9b
UniProtKB AC	P0DTD2 (CoV2)
Comment	SARS-CoV protein 9b is a virion-associated accessory protein [14] that acts to block the host's ability to mount an antiviral IFN-induced innate immune response [9]. By homology, 9b from SARS-CoV-2 would be predicted to exhibit a similar function.

SARS-CoV-2 Protein non-structural 7b Show summary »« Hide summary More detailed page

Target Id	3123
Nomenclature	SARS-CoV-2 Protein non-structural 7b
Previous and unofficial names	nsp7b \| Accessory protein 7b
UniProtKB AC	P0DTD8 (CoV2)
Comment	Protein 7b is a coronavirus accessory protein. Experimental evidence suggests that SARS-CoV 7b has some attenuating function [6]. By homology, SARS-CoV-2 7b is likely to have a similar function.

SARS-CoV-2 Replicase polyprotein 1a Show summary »« Hide summary More detailed page

Target Id	3124
Nomenclature	SARS-CoV-2 Replicase polyprotein 1a
UniProtKB AC	Replicase polyprotein 1ab (CoV2)
Comment	The replicase polyprotein 1a (pp1a) encodes a set of 11 smaller proteins, including two proteases that are responsible for cleaving the polyprotein chain into its component parts. The components are in the main, non-structural and are involved in the transcription and replication of viral RNA.

SARS-CoV-2 Replicase polyprotein 1ab Show summary »« Hide summary More detailed page

Target Id	3125
Nomenclature	SARS-CoV-2 Replicase polyprotein 1ab
UniProtKB AC	P0DTD1 (CoV2)
Comment	The replicase polyprotein 1ab (pp1ab) encodes a set of 15 smaller proteins (5 more than pp1a), including two proteases that are responsible for cleaving the polyprotein chain into its component parts. The components are in the main, non-structural and are involved in the transcription and replication of viral RNA.

SARS-CoV-2 Spike glycoprotein Show summary »« Hide summary More detailed page

Target Id	3114
Nomenclature	SARS-CoV-2 Spike glycoprotein
Previous and unofficial names	spike protein
UniProtKB AC	P0DTC2 (CoV2)

References

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1. Cottam EM, Whelband MC, Wileman T. (2014) Coronavirus NSP6 restricts autophagosome expansion. Autophagy, 10 (8): 1426-41. [PMID:24991833]

2. Fan H, Ooi A, Tan YW, Wang S, Fang S, Liu DX, Lescar J. (2005) The nucleocapsid protein of coronavirus infectious bronchitis virus: crystal structure of its N-terminal domain and multimerization properties. Structure, 13 (12): 1859-68. [PMID:16338414]

3. Hilgenfeld R. (2014) From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design. FEBS J., 281 (18): 4085-96. [PMID:25039866]

4. Imbert I, Guillemot JC, Bourhis JM, Bussetta C, Coutard B, Egloff MP, Ferron F, Gorbalenya AE, Canard B. (2006) A second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus. EMBO J., 25 (20): 4933-42. [PMID:17024178]

5. Pervushin K, Tan E, Parthasarathy K, Lin X, Jiang FL, Yu D, Vararattanavech A, Soong TW, Liu DX, Torres J. (2009) Structure and inhibition of the SARS coronavirus envelope protein ion channel. PLoS Pathog., 5 (7): e1000511. [PMID:19593379]

6. Pfefferle S, Krähling V, Ditt V, Grywna K, Mühlberger E, Drosten C. (2009) Reverse genetic characterization of the natural genomic deletion in SARS-Coronavirus strain Frankfurt-1 open reading frame 7b reveals an attenuating function of the 7b protein in-vitro and in-vivo. Virol. J., 6: 131. [PMID:19698190]

7. Pillaiyar T, Manickam M, Namasivayam V, Hayashi Y, Jung SH. (2016) An Overview of Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy. J. Med. Chem., 59 (14): 6595-628. [PMID:26878082]

8. Ruch TR, Machamer CE. (2012) The coronavirus E protein: assembly and beyond. Viruses, 4 (3): 363-82. [PMID:22590676]

9. Shi CS, Qi HY, Boularan C, Huang NN, Abu-Asab M, Shelhamer JH, Kehrl JH. (2014) SARS-coronavirus open reading frame-9b suppresses innate immunity by targeting mitochondria and the MAVS/TRAF3/TRAF6 signalosome. J. Immunol., 193 (6): 3080-9. [PMID:25135833]

10. Surya W, Li Y, Verdià-Bàguena C, Aguilella VM, Torres J. (2015) MERS coronavirus envelope protein has a single transmembrane domain that forms pentameric ion channels. Virus Res., 201: 61-6. [PMID:25733052]

11. Tan YJ, Fielding BC, Goh PY, Shen S, Tan TH, Lim SG, Hong W. (2004) Overexpression of 7a, a protein specifically encoded by the severe acute respiratory syndrome coronavirus, induces apoptosis via a caspase-dependent pathway. J. Virol., 78 (24): 14043-7. [PMID:15564512]

12. te Velthuis AJ, van den Worm SH, Snijder EJ. (2012) The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension. Nucleic Acids Res., 40 (4): 1737-47. [PMID:22039154]

13. Wilson L, McKinlay C, Gage P, Ewart G. (2004) SARS coronavirus E protein forms cation-selective ion channels. Virology, 330 (1): 322-31. [PMID:15527857]

14. Xu K, Zheng BJ, Zeng R, Lu W, Lin YP, Xue L, Li L, Yang LL, Xu C, Dai J et al.. (2009) Severe acute respiratory syndrome coronavirus accessory protein 9b is a virion-associated protein. Virology, 388 (2): 279-85. [PMID:19394665]

15. Zhang R, Wang K, Lv W, Yu W, Xie S, Xu K, Schwarz W, Xiong S, Sun B. (2014) The ORF4a protein of human coronavirus 229E functions as a viroporin that regulates viral production. Biochim. Biophys. Acta, 1838 (4): 1088-95. [PMID:23906728]

NC-IUPHAR subcommittee and family contributors

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How to cite this family page

Database page citation (select format):

Concise Guide to PHARMACOLOGY citation:

Alexander SPH, Kelly E, Mathie A, Peters JA, Veale EL, Armstrong JF, Faccenda E, Harding SD, Pawson AJ, Sharman JL, Southan C, Buneman OP, Cidlowski JA, Christopoulos A, Davenport AP, Fabbro D, Spedding M, Striessnig J, Davies JA; CGTP Collaborators. (2019) The Concise Guide to PHARMACOLOGY 2019/20: Introduction and Other Protein Targets. Br J Pharmacol. 176 Issue S1: S1-S20.