Coronaviruses (CoVs) are enveloped positive-strand RNA viruses that infect
many species, including humans, other mammals, and birds. After infection, the
host may develop respiratory, bowel, liver, and neurological diseases.
Coronaviruses are divided into four genera: αcoronavirus, βcoronavirus,
γcoronavirus, and Deltacoronavirus. The ideal hosts of αCoV and
βCoV are mammals, and γCoV primarily infects birds, while DeltaCoV has
been identified in both mammals and birds. SARS, SARS-CoV-2, BatCoV RaTG13 and
Bat-SARS-like coronavirus (BATSL-CoVZXC21 and BAT-SL-CoVZC45) belong to the
Sarbecovirus subgenus of βCoV [E1].
The CoV replicase gene encodes two overlapping polyproteins, termed pp1a and
pp1ab, which mediate viral replication and transcription. The polypeptides
pp1a and pp1ab are processed by the action of a main protease (Nsp5) (see
<PDOC51442>) and of one or two papain-like proteases (PLpro) (see <PDOC51124>)
found in Nsp3 into non-structural proteins (Nsps) to form the replication/
transcription complex (RTC). Among them, the Nsp12 RNA-dependent RNA
polymerase, that includes an RdRp catalytic domain conserved in all RNA
viruses (see <PDOC50507>), possesses some minimal activity on its own, but the
addition of the Nsp7 and Nsp8 cofactors greatly stimulates polymerase
activity (see <PDOC51948>). The Nsp12-Nsp7-Nsp8 subcomplex is thus defined as
the minimal core component for mediating CoV RNA synthesis with additional
Nsps playing roles in RNA modification. Nsp9 is known to colocalize with Nsp7,
Nsp8 and Nsp10 within the replication complex and is presumed to play a role
in RNA replication. Nsp9 is able to bind single-stranded (ss)DNA or ssRNA,
although binding of ssRNA is expected to be the native function. The Nsp9
ssRNA-binding domain is indispensable for viral RNA replication. The CoV Nsp9
ssRNA-binding domain is a seemingly obligate homodimer but CoV Nsp9 ssRNA-binding domains have diverse forms of dimerization that promote their
biological function. Using diverse dimerization strategies, the Nsp9 ssRNA-binding domain might increase the nucleic acid binding interface and then
promote its nucleic acid binding affinity, which might stabilize nascent viral
RNAs during replication or transcription, thus providing protection from
nucleases [1,2,3,4,5,6].
The Nsp9 ssRNA-binding domain contains seven antiparallel β-strands and an
α-helix that are arranged into a single compact domain and form a cone-shaped β-barrel flanked by the C-terminal α-helix (see <PDB:1QZ8>). All
seven β-strands form a β-sandwich, with sheet β1-3 interleaved
between sheets β4-5 and β6-7. The N- and C-termini of the domain are
more conserved than the central core region, and the GXXXG motif is strictly
conserved. The CoV Nsp9 ssRNA-binding domain forms a dimer through the
interaction of parallel α-helices containing the protein-protein
interaction motif GXXXG [2,3,4,5,6].
The profile we developed covers the entire CoV Nsp9 ssRNA-binding domain.
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