The RNAs and Proteins of dsRNA Viruses


Edited by Peter. P. C. Mertens, Houssam Attoui and Dennis H. Bamford

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The dsRNA segments and proteins of simian rotavirus A / SA11 

(genus Rotavirus: family Reoviridae

(available as a Word file )   

 Coding assignments,  virion locations of rotavirus proteins and 3D structure.


Structural studies [17, 31, 37, 72, 73, 88, 89]: last updated April 2003, references in [square brackets]



Genome Segment

Size (bp)




Gene Product(s)

(': Protein Function)

Protein Size

Location in Virus Particle

Copy Number/


Cognate Proteins

GenBank Accession Number (s)

Functions and Properties




VP1 (Pol)

1088 aa


125,005 Da

Inner capsid, 5-fold axis


Orthoreovirus l3(Pol)

Orbivirus VP 1(Pol)

Coltivirus VP1(Pol)

Cypovirus Pol



RNA-dependent RNA polymerase [87].

Part of minimal replication complex [63,87],

Virus specific 3’-mRNA binding [61,62]

Part of virion transcription complex with VP3 [11,73]





VP2 (T1)

881 aa


102,431 Da

Inner capsid


Orbivirus: VP3

Orthoreovirus: l1



Inner capsid structural protein [8].

Non-specific ss & dsRNA-binding activity [10]

Myristoylated [15].

Cleaved [23,86].

Part of minimal replication complex [63].

Leucine zipper [56].

Interacts with VP5 [7].




VP3 (Cap)

835 aa


98,120 Da

Inner capsid, 5-fold axis


Orbivirus: VP4

Orthoreovirus: l2






Guanylyltransferase [45,68].

Methyltransferase [13].

Basic Protein [44,56].

Part of virion transcription complex with VP1 [11,73].

Non-specific ssRNA binding [62].



10 -2337


776 aa


Outer capsid spike








VP4 Dimers form outer capsid spike [3].

Interacts with VP6 [89].

Virus infectivity enhanced by trypsin cleavage of VP4 into VP5* and VP8* [22,46].

Hemagglutinin [26,38].

Cell attachment protein [47,75,85].

P-type neutralization antigen [32,58].

VP5* permeabilizes membranes [16].

Crystal structure of VP8 fragment (galectin fold) [19].

TRAF2 signaling [43].

Protection [33].



529 aa



60,000 Da





247 aa



28,000 Da







495 aa


58,654 Da









Associates with cytoskeleton [34].

Extensive sequence diversity between strains [20,42,57].

Two conserved cysteine-rich zinc-finger motifs [57,60].

Virus specific 5’-mRNA binding [34,62].

Interacts with host IFN regulatory factor 3 [29].




VP6 (T13)

397 aa


48,160 Da

Middle capsid


Orbivirus: VP7







M27824 [76]

Major virion protein [49,72].

Middle capsid structural protein [72].

Homotrimeric 4o structure [72].

Subgroup antigen [30,39].

Myristoylated [15].

Protection (? Mechanism) [11,84].

Crystal structure [50].

Hydrophobic [48,76].





315 aa


34,600 Da






Homodimer [51,66].

Virus-specific 3’- mRNA binding [69,70].

Binds eIF4G1 and circularizes mRNA on initiation complex [67].

Involved in translational regulation and host shut-off [14,59,82].

Crystal structure: NSP3 NH3 fragment with 3’- viral RNA [17] and NSP3 COOH fragment with eIF4G fragment [31].





317 aa


36,700 Da



Orbivirus: NS2

Orthoreovirus: sNS

L04531 [64]

Non-specific ssRNA-binding [41,62]

Accumulates in viroplasm [65]

Involved in viroplasm formation with NSP5 [25]

NTPase activity [79]

Helix destabilization activity [78]

Functional octamer [79,80]

Binds NSP5 and VP1 [1, 40]

Regulates NSP5 autophosphorylation [1]

Crystal structure (HIT-like fold) [37]





326 aa


37,368 Da

Outer capsid glycoprotein





Outer capsid structural glycoprotein [21,49].

G-type neutralization antigen [32].

N-linked high mannose glycosylation and trimming [21].

RER transmembrane protein, cleaved signal sequence [22].

Ca2+ binding [18].

Protection [33].

Mediates membrane penetration [91]





175 aa


20,290 Da




AF087678 [9]

Enterotoxin [6].

Receptor for budding of double-layer particle through ER membrane [5, 53].

RER transmembrane glycoprotein [22].

Ca++/ Sr++ binding site [36].

N-linked high mannose glycosylation [21].

Protection [24].

Host cell [Ca2+]i mobilization [81].





198 aa


21,725 Da







M28347 [83]

Interacts with VP2, NSP2 and NSP6 [1, 27].

Homomultimerizes [27,71].

O-linked glycosylation [28].

(Hyper-) Phosphorylated [2, 83, 90]. Autocatalytic kinase activity enhanced by NSP2 interaction [2].

Non-specific ssRNA binding [52,62].



92 aa


11,012 Da




Product of second, out-of-frame ORF [52].

Interacts with NSP5 [27].

Localizes to viroplasm [52].

': Protein structure/function: RNA polymerase = A(Pol)@; capping enzyme = A(CaP)@; Inner virus structural protein with T = 13 symmetry = A(T13)"; viral inclusion body or viroplasm matrix protein = A(ViP)@. Other species within the genus may have proteins with significant differences in sizes.


Segments numbered based on migration of SA11 genome segments in SDS-PAGE gel. Migration order may differ among other members of the genus.


‡ Proteins with similar functions from other genera.


Updated April 2003, by R.F. Ramig & M.K. Estes


(from : The RNAs and Proteins of dsRNA Viruses:  Edited by Peter. P. C. Mertens and Dennis H. Bamford 

Please make suggestions for changes or updates to this table by e-mail to Peter Mertens

Reference List

1. Afrikanova, I., E. Fabbretti, M.C. Miozzo, and O.R. Burrone. 1998. Rotavirus NSP5 phosphorylation is up-regulated by interaction with NSP2. Journal of General Virology 79:2679-2686.


2. Afrikanova, I., M.C. Miozzo, S. Giambiagi, and O. Burrone. 1996. Phosphorylation generates different forms of rotavirus NSP5. Journal of General Virology 77:2059-2065.


3. Anthony, I.D., S. Bullivant, S. Dayal, A.R. Bellamy, and J.A. Berriman. 1991. Rotavirus spike structure and polypeptide composition. J.Virol. 65:4334-4340.


4. Arias, C.F., S. L:opez, J.R. Bell, and J.H. Strauss. 1984. Primary structure of the neutralization antigen of simian rotavirus SA11 as deduced from cDNA sequence. J.Virol. 50:657-661.

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  3. Berois, M., C. Sapin, I. Erk, D. Poncet, and J. Cohen. 2003. Rotavirus nonstructural protein NSP5 interacts with major core protein VP2. J. Virol. 77: 1757-1763.

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  5. Both, G.W., L.J. Siegman, A.R. Bellamy, and P.H. Atkinson. 1983. Coding assignment and nucleotide sequence of simian rotavirus SA11 gene segment 10: location of glycosylation sites suggests that the signal peptide is not cleaved. J.Virol. 48:335-339.

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  9. Chen, D.Y., C.L. Luongo, M.L. Nibert, and J.T. Patton. 1999. Rotavirus open cores catalyze 5'-capping and methylation of exogenous RNA: Evidence that VP3 is a methyltransferase. Virology 265:120-130.

  10. Chizhikov V. and J.T. Patton. 2000. A four-nucleotide translation enhancer in the 3'-terminal consensus sequence of the nonpolyadenylated mRNAs of rotavirus. RNA 6: 814-825.

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  27. Groft C.M. and S.K. Burley. 2002. Recognition of eIF4G by rotavirus NSP3 reveals a basis for mRNA circularization. Mol. Cell 9: 1273-1283.

  28. Hoshino, Y., M.M. Sereno, K. Midthun, J. Flores, A.Z. Kapikian, and R.M. Chanock. 1985. Independent segregation of two antigenic specificities (VP3 and VP7) involved in neutralization of rotavirus infectivity. Proc.Natl.Acad.Sci.U.S.A. 82:8701-8704.

  29. Hoshino,Y. and A.Z. Kapikian. 1996. Classification of rotavirus VP4 and VP7 serotypes. Arch. Virol. [Suppl] 12: 99-111.

  30. Hua, J., X. Chen, and J.T. Patton. 1994. Deletion mapping of the rotavirus metalloprotein NS53 (NSP1): The conserved cysteine-rich region is essential for virus- specific RNA binding. Journal of Virology 68:3990-4000.

  31. Hua, J., E.A. Mansell, and J.T. Patton. 1993. Comparative analysis of the rotavirus NS53 gene: Conservation of basic and cysteine-rich regions in the protein and possible stem-loop structures in the RNA. Virology 196:372-378.

  32. Jagannath, M.R., R.R. Vethanayagam, B.S. Reddy, S. Raman, and C.D. Rao. 2000. Characterization of human symptomatic rotavirus isolates MP409 and MP480 having 'long' RNA electropherotype and subgroup I specificity, highly related to the P6[1],G8 type bovine rotavirus A5, from Mysore, India. Archives of Virology 145:1339-1357.

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  34. Kalica, A.R., J. Flores, and H.B. Greenberg. 1983. Identification of the rotaviral gene that codes for hemagglutination and protease-enhanced plaque formation. Virology. 125:194-205.

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  36. Kattoura, M.D., X. Chen, and J.T. Patton. 1994. The rotavirus RNA-binding protein NS35 (NSP2) forms 10S multimers and interacts with the viral RNA polymerase. Virology 202:803-813.

  37. Kattoura, M.D., L.L. Clapp, and J.T. Patton. 1992. The rotavirus nonstructural protein, NS35, possesses RNA- binding activity in vitro and in vivo. Virology 191:698-708.

  38. Kojima, K., K. Taniguchi, and N. Kobayashi. 1996. Species-specific and interspecies relatedness of NSP1 sequences in human, porcine, bovine, feline, and equine rotavirus strains. Archives of Virology 141:1-12.

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  41. Liu, M., N.M. Mattion, and M.K. Estes. 1992. Rotavirus VP3 expressed in insect cells possesses guanylyltransferase activity. Virology 188:77-84.

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  43. Ludert, J.E., N.G. Feng, J.H. Yu, R.L. Broome, Y. Hoshino, and H.B. Greenberg. 1996. Genetic mapping indicates that VP4 is the rotavirus cell attachment protein in vitro and in vivo. Journal of Virology 70:487-493.

  44. Mansell, E.A., R.F. Ramig, and J.T. Patton. 1994. Temperature-sensitive lesions in the capsid proteins of the rotavirus mutants tsF and tsG that affect virion assembly. Virology 204:69-81.

  45. Mason, B.B., D.Y. Graham, and M.K. Estes. 1980. In vitro transcription and translation of simian rotavirus SA11 gene products. J.Virol. 33:1111-1121.

  46. Mathieu, M., I. Petitpas, J. Navaza, J. Lepault, E. Kohli, P. Pothier, B.V.V. Prasad, J. Cohen and F.A. Rey. 2001. Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion. EMBO J. 20: 1485-1497.

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(The RNAs and Proteins  of dsRNA Viruses:  Edited by Peter. P. C. Mertens, Houssam Attoui and Dennis H. Bamford)