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various levels (Walsh and Mohr, 2011). To date, functional stud- papain-like protease (PLP) domains, PLP1 and PLP2, as well
ies of most of these nsps were conducted with other members as a transmembrane domain (Kanjanahaluethai et al., 2007).
of the family Coronaviridae, and the demonstrated functions of This transmembrane domain has been demonstrated to play a
these proteins are discussed as follows. significant role in tethering PLP2 during processing at cleavage
To inhibit host protein translation, many alpha- and betac- site 3, as well as mediating the ER membrane association of cyto-
oronaviruses encode nsp1, which works to selectively induce solic proteins (Kanjanahaluethai et al., 2007). Besides acting as
host RNA degradation and acts as an interferon antagonist a protease in polyprotein processing, nsp3 can also function as
(Kamitani et al., 2006; Lokugamage et al., 2012). Interestingly, a deubiquitinating enzyme to degrade polyubiquitin-associated
gamma- and deltacoronaviruses do not encode nsp1, but there proteins in the host antiviral signalling pathway (Yu et al., 2017),
is early evidence in IBV suggesting that these CoVs can continue as well as an interferon antagonist (Yang et al., 2014).
to induce host shutoff via accessory proteins by antagonizing the Nsp4 was reported to be localized at the ER and engages in
host innate immune response (Kint et al., 2016). homotypic and heterotypic interactions with nsp3 and nsp6,
Downstream of nsp1 is nsp2, a 65 kDa protein in its mature respectively (Hagemeijer et al., 2011). It assembles in the mem-
form (Denison et al., 1995). The counterpart in IBV is an 87 kDa brane as a tetraspanning transmembrane protein with a N endo /
protein, which is the N-terminal cleavage product of polyproteins C endo topology and appears to play a role in the early secretory
1a and 1ab (Liu et al., 1994). Deletion of nsp2 in MHV and pathway in replication (Oostra et al., 2007). IBV nsp4 is post-
SARS-CoV through reverse genetics have found this protein to be translationally modified by glycosylation (Lim and Liu, 1998a,b).
dispensable in viral replication, as infectious mutants have been Nsp5 encodes a 3C-like protease (3CLpro), or also known as
recovered with intact polyprotein processing, albeit with defects the main protease (Mpro). It is responsible for all downstream
in RNA synthesis and growth kinetics (Graham et al., 2005). cleavage events beyond nsp4. Nsp5 exists as a three-domain
However, IBV nsp2 has been known to act as a protein kinase R structure containing a chymotrypsin-like fold formed by domains
(PKR) antagonist (Wang, X. et al., 2009), and may play a role in 1 and 2. Domain 3 appears to be crucial for nsp5 dimerization,
inhibiting the dsRNA-triggered RNase L system. although the function of this domain remains to be investigated
MHV nsp3 is a multi-domain protein, containing two (Anand et al., 2002). Since Mpro is only active as a homodimer,

Table 5.2 Functions and structures of coronavirus non-structural proteins. With the exception of nsp11, the enzymatic functions of each
coronavirus nsp have been confirmed. Structures for nsp2, nsp12, and nsp13 has not yet been solved. Nsp11 is not known to produce
protein, and therefore do not have a structure
Non-structural
protein Function PDB ID Method Coronavirus References
1 IFN antagonist 2HSX NMR SARS-CoV Almeida et al.
(2007)
2 IFN antagonist
3 Papain-like protease (PL ) for polyprotein processing, 2FE8 X-ray SARS-CoV Ratia et al.
pro
deubiquitinas, IFN antagonist diffraction (2006)
4 Transmembrane scaffold
5 Main protease (M , 3CL ) for polyprotein processing, IFN 2BX3 X-ray SARS-CoV Tan et al.
pro pro
antagonist diffraction (2005)
6 Transmembrane scaffold
7 Hexadecameric complex 2KYS NMR SARS-CoV Johnson et al.
(2010)
8 Hexadecameric complex; primase 2AHM X-ray SARS-CoV Zhai et al.
diffraction (2005)
9 RNA-binding protein 2J97 X-ray HCoV-229E Ponnusamy et
diffraction al. (2008)
10 Zinc-binding domain (ZBD), 2′-O-methyltransferase 2FYG X-ray SARS-CoV Joseph et al.
(2′-O-MTase) cofactor diffraction (2006)
11 Unknown
12 RNA-dependent RNA polymerase (RdRP)
13 ZBD, RNA 5′triphosphatase, RNA helicase
14 3′–5′ exoribonuclease (ExoN), 7-methyltransferase 5C8U X-ray SARS-CoV Ma et al.
diffraction (2015)
15 Endoribonuclease (NendoU) 2H85 X-ray SARS-CoV Ricagno et al.
diffraction (2006)
16 2′-O-MTase 2XYR X-ray SARS-CoV Decroly et al.
diffraction (2011)