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)

 

 

ORFs

Gene Product(s)

(': Protein Function)

Protein Size

Location in Virus Particle

Copy Number/

Particle

Cognate Proteins‡

GenBank Accession Number (s)

Functions and Properties

1

(3302)

18-3282

VP1 (Pol)

1088 aa

 

125,005 Da

Inner capsid, 5-fold axis

12

Orthoreovirus l3(Pol)

Orbivirus VP 1(Pol)

Coltivirus VP1(Pol)

Cypovirus Pol

X16830

[56]

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]

2

(2690)

 

17-2659

VP2 (T1)

881 aa

 

102,431 Da

Inner capsid

120

Orbivirus: VP3

Orthoreovirus: l1

X16831

[56]

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].

3

(2591)

50-2554

VP3 (Cap)

835 aa

 

98,120 Da

Inner capsid, 5-fold axis

12

Orbivirus: VP4

Orthoreovirus: l2

X16062

[44]

 

X16387

[56]

Guanylyltransferase [45,68].

Methyltransferase [13].

Basic Protein [44,56].

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

Non-specific ssRNA binding [62].

4

(2362)

10 -2337

VP4

776 aa

86,782

Outer capsid spike

120

-

D16346

[77]

 

X14204

[55]

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].

-

VP5*

529 aa

(247-776)

 

60,000 Da

 

 

-

VP8*

247 aa

(1-247)

 

28,000 Da

 

 

5

(1611)

31-1515

NSP1

495 aa

 

58,654 Da

Nonstructural

0

-

L18944

[35]

 

X14914

[57]

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].

6

[1356]

24-1214

VP6 (T13)

397 aa

 

48,160 Da

Middle capsid

780

Orbivirus: VP7

L15384

[48]

 

L33365

[48]

 

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].

7

(1105)

26-970

NSP3

315 aa

 

34,600 Da

Nonstructural

0

-

M87502

[51]

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].

8

(1059)

47-997

NSP2 (VIP)

317 aa

 

36,700 Da

Nonstructural

0

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]

9

(1062)

49-1026

VP7

326 aa

 

37,368 Da

Outer capsid glycoprotein

780

-

K02028

[4]

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]

10

(751)

41-569

NSP4

175 aa

 

20,290 Da

Nonstructural

0

-

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].

11

(667)

22-615

NSP5

198 aa

 

21,725 Da

Nonstructural

0

-

X07831

[54]

 

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].

80-355

NSP6

92 aa

 

11,012 Da

Nonstructural

0

-

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 peter.mertens@bbsrc.ac.uk

Reference List

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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.

 

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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.

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