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PROSITE documentation PDOC51951

Coronavirus (CoV) Nsp9 ssRNA-binding domain profile


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.

Last update:

December 2020 / First entry.


Technical section

PROSITE method (with tools and information) covered by this documentation:

COV_NSP9_SSRNA_BD, PS51951; Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile  (MATRIX)


1AuthorsGorgulla C. Das K.M.P. Leigh K.E. Cespugli M. Fischer P.D. Wang Z.-F. Tesseyre G. Pandita S. Shnapir A. Calderaio A. Hutcheson C. Gechev M. Rose A. Lewis N. Yaffe E. Luxenburg R. Herce H.D. Durmaz V. Halazonetis T.D. Fackeldey K. Patten J.J. Chuprina A. Dziuba I. Plekhova A. Moroz Y. Radchenko D. Tarkhanova O. Yavnyuk I. Gruber C.C. Yust R. Payne D. Naeaer A.M. Namchuk M.N. Davey R.A. Wagner G. Kinney J. Arthanari H.
TitleA Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening.
SourceChemRxiv 0:0-0(2020).
PubMed ID33200116

2AuthorsEgloff M.-P. Ferron F. Campanacci V. Longhi S. Rancurel C. Dutartre H. Snijder E.J. Gorbalenya A.E. Cambillau C. Canard B.
TitleThe severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world.
SourceProc. Natl. Acad. Sci. U. S. A. 101:3792-3796(2004).
PubMed ID15007178

3AuthorsPonnusamy R. Moll R. Weimar T. Mesters J.R. Hilgenfeld R.
TitleVariable oligomerization modes in coronavirus non-structural protein 9.
SourceJ. Mol. Biol. 383:1081-1096(2008).
PubMed ID18694760

4AuthorsMiknis Z.J. Donaldson E.F. Umland T.C. Rimmer R.A. Baric R.S. Schultz L.W.
TitleSevere acute respiratory syndrome coronavirus nsp9 dimerization is essential for efficient viral growth.
SourceJ. Virol. 83:3007-3018(2009).
PubMed ID19153232

5AuthorsZeng Z. Deng F. Shi K. Ye G. Wang G. Fang L. Xiao S. Fu Z. Peng G.
TitleDimerization of Coronavirus nsp9 with Diverse Modes Enhances Its Nucleic Acid Binding Affinity.
SourceJ. Virol. 92:0-0(2018).
PubMed ID29925659

6AuthorsLittler D.R. Gully B.S. Colson R.N. Rossjohn J.
TitleCrystal Structure of the SARS-CoV-2 Non-structural Protein 9, Nsp9.
SourceiScience 23:101258-101258(2020).
PubMed ID32592996


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