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PR00233

Identifier
ICOSAHEDRAL  [View Relations]  [View Alignment]  
Accession
PR00233
No. of Motifs
3
Creation Date
11-MAR-1995  (UPDATE 27-JUN-1999)
Title
Icosahedral viral capsid protein signature
Database References

PROSITE; PS00555 ICOSAH_VIR_COAT_S
BLOCKS; BL00555
PFAM; PF00729 Viral_coat
INTERPRO; IPR000937
PDB; 2TBV
SCOP; 2TBV
CATH; 2TBV
Literature References
1. TIMMINS, P.A., WILD, D. AND  WITZ, J.
The three-dimensional distribution of RNA and protein in the interior
of tomato bushy stunt virus: a neutron low-resolution single-crystal
diffraction study.
STRUCTURE 2 1191-1201 (1994).
 
2. DOLJA, V.V. AND KOONIN, E.V.
Phylogeny of capsid proteins of small icosahedral RNA plant viruses.
J.GEN.VIROL. 72 1481-1486 (1991).

Documentation
The capsid proteins of plant icosahedral positive strand RNA viruses
form 4 different domains: a positively charged, N-terminal `R' domain,
which interacts with RNA (66 residues); a connecting arm, `a' (35
residues); a central, surface `S' domain, which forms the virion shell
(170 residues); and a projecting, C-terminal `P' domain [1].
 
The S domain comprises 8 anti-parallel beta-strands, which form a 
twisted sheet or jelly-roll fold. This structure is shared by a number
of plant viral capsid proteins, including carmoviruses, dianthoviruses,
sobemoviruses, tombusviruses and tobacco necrosis virus [2].
 
ICOSAHEDRAL is a 3-element fingerprint that provides a signature for
icosahedral virus capsid proteins. The fingerprint was derived from an
initial alignment of 11 sequences: the motifs were drawn from conserved
regions within the S domain, motifs 2 and 3 spanning the region encoded
by PROSITE pattern ICOSAH_VIR_COAT_S (PS000555), which encompasses the
third and fourth beta strands of the jelly-roll. Two iterations on OWL25.2
were required to reach convergence, at which point a true set comprising
24 sequences was identified. Three partial matches were also found, all
family members lacking significant matches with wither motif 1 or 3.
 
An update on SPTR37_9f identified a true set of 36 sequences.
Summary Information
36 codes involving  3 elements
0 codes involving 2 elements
Composite Feature Index
3363636
2000
123
True Positives
COAT_AMCV     COAT_CARMV    COAT_CNV      COAT_CRV      
COAT_MNSV COAT_RCNMV COAT_SBMV COAT_TBSVB
COAT_TBSVC COAT_TCV COAT_TNVA COAT_TNVD
O12304 O15850 O41351 O56987
O72158 O72160 P89111 P89212
Q65990 Q66098 Q66102 Q66226
Q83095 Q83106 Q83427 Q83428
Q83473 Q83928 Q83942 Q84832
Q86586 Q87030 Q88611 Q89761
Sequence Titles
COAT_AMCV   COAT PROTEIN - ARTICHOKE MOTTLED CRINKLE VIRUS (AMCV). 
COAT_CARMV COAT PROTEIN - CARNATION MOTTLE VIRUS (CARMV).
COAT_CNV COAT PROTEIN - CUCUMBER NECROSIS VIRUS (CNV).
COAT_CRV COAT PROTEIN - CYMBIDIUM RINGSPOT VIRUS.
COAT_MNSV COAT PROTEIN - MELON NECROTIC SPOT VIRUS (MNSV).
COAT_RCNMV COAT PROTEIN (CAPSID PROTEIN) - RED CLOVER NECROTIC MOSAIC VIRUS (RCNMV).
COAT_SBMV COAT PROTEIN PRECURSOR (CAPSID PROTEIN) - SOUTHERN BEAN MOSAIC VIRUS (SBMV).
COAT_TBSVB COAT PROTEIN - TOMATO BUSHY STUNT VIRUS (STRAIN BS-3) (TBSV).
COAT_TBSVC COAT PROTEIN (P41 CAPSID PROTEIN) - TOMATO BUSHY STUNT VIRUS (STRAIN CHERRY) (TBSV).
COAT_TCV COAT PROTEIN - TURNIP CRINKLE VIRUS (TCV).
COAT_TNVA COAT PROTEIN - TOBACCO NECROSIS VIRUS (STRAIN A) (TNV).
COAT_TNVD COAT PROTEIN - TOBACCO NECROSIS VIRUS (STRAIN D) (TNV).
O12304 CAPSID PROTEIN - GALINSOGA MOSAIC CARMOVIRUS.
O15850 L3162.1 PROTEIN - LEISHMANIA MAJOR.
O41351 29 KDA COAT PROTEIN - TOBACCO NECROSIS VIRUS.
O56987 COAT PROTEIN - PELARGONIUM FLOWER BREAK VIRUS.
O72158 COAT PROTEIN - SOUTHERN BEAN MOSAIC VIRUS (SBMV).
O72160 COAT PROTEIN - SOUTHERN BEAN MOSAIC VIRUS (SBMV).
P89111 CAPSID PROTEIN - SAGUARO CACTUS VIRUS.
P89212 41K PROTEIN - TOMATO BUSHY STUNT VIRUS.
Q65990 COAT PROTEIN - CARDAMINE CHLOROTIC FLECK VIRUS.
Q66098 P37K PROTEIN - CARNATION RINGSPOT VIRUS.
Q66102 CAPSID PROTEIN - CARNATION ITALIAN RINGSPOT VIRUS.
Q66226 TRANSLATED REGION - CYMBIDIUM RINGSPOT VIRUS.
Q83095 VIRAL COAT PROTEIN - LUCERNE TRANSIENT STREAK VIRUS.
Q83106 CAPSID PROTEIN - LEEK WHITE STRIPE VIRUS.
Q83427 COAT PROTEIN - MELON NECROTIC SPOT VIRUS (MNSV).
Q83428 COAT PROTEIN - MELON NECROTIC SPOT VIRUS (MNSV).
Q83473 COAT PROTEIN - SOUTHERN BEAN MOSAIC VIRUS (SBMV).
Q83928 COAT PROTEIN (P48) - UNIDENTIFIED.
Q83942 CAPSID PROTEIN - OLIVE LATENT VIRUS 1.
Q84832 CAPSID PROTEIN - POTHOS LATENT VIRUS.
Q86586 COAT PROTEIN - PELARGONIUM LEAF CURL VIRUS.
Q87030 UNIDENTIFIED GENES, THREE COMPLETE CDS'S INCLUDING FUSION PROTEIN - SWEET CLOVER NECROTIC MOSAIC VIRUS.
Q88611 COAT PROTEIN - TOBACCO NECROSIS VIRUS.
Q89761 CAPSID - COWPEA MOTTLE VIRUS.
Scan History
OWL25_2    2  150  NSINGLE    
SPTR37_9f 4 100 NSINGLE
Initial Motifs
Motif 1  width=15
Element Seqn Id St Int Rpt
LASNFDQYSFNSVVL NRL_2TBVA1 47 47 -
LASNFDQYSFNSVVL NRL_2TBVB 47 47 -
QSQMWNTIVFNSVRI P11642 94 94 -
IASNFDQYTFNSVVL COAT_TBSVC 148 148 -
LASNFDQYSFNSVVL COAT_TBSVB 148 148 -
IAANFDQYKFNSLRF COAT_CNV 140 140 -
LASNFDQYMFNTLRL COAT_CRV 144 144 -
QAQLYDMYRFTRLRI COAT_MNSV 141 141 -
EAAQYEKYRFTSLRF COAT_TCV 122 122 -
VAQNWSKYAWVAIRY COAT_SBMV 122 122 -
LATNFNKYRITALTV COAT_CARMV 123 123 -

Motif 2 width=17
Element Seqn Id St Int Rpt
YSPMSPSTTGGKVALAF COAT_TCV 138 1 -
YLPSCPTTTSGAIHMGF COAT_SBMV 138 1 -
YSPACSFETNGRVALGF COAT_CARMV 139 1 -
YVPLCGTTEVGRVALYF NRL_2TBVA1 63 1 -
YVPLCGTTEVGRVALYF NRL_2TBVB 63 1 -
WETFTADTTSGYISMAF P11642 110 1 -
YVPLCSTTEVGRVAIYF COAT_TBSVC 164 1 -
YVPLCGTTEVGRVALYF COAT_TBSVB 164 1 -
YVPLVNTTTNGRVALYF COAT_CNV 156 1 -
YVPMCATTETGRVAIYF COAT_CRV 160 1 -
YIPTTGSTSTGRVSLLW COAT_MNSV 157 1 -

Motif 3 width=17
Element Seqn Id St Int Rpt
DSQDPEPADRVELANFG COAT_TBSVB 183 2 -
DSQDLEPVDRIELANMR COAT_CRV 179 2 -
DSQDPLPIDRAAISSYA COAT_MNSV 176 2 -
DAAKPPPNDLASLYNIE COAT_TCV 157 2 -
DMADTLPVSVNQLSNLK COAT_SBMV 157 2 -
DASDTPPTTKVGFYDLG COAT_CARMV 158 2 -
DSQDPEPADRVELANFG NRL_2TBVA1 82 2 -
DSQDPEPADRVELANFG NRL_2TBVB 82 2 -
DYMLSIPTGVEDVARIV P11642 129 2 -
DSEDPEPADRVELANYS COAT_TBSVC 183 2 -
DSEDPGPDDRAALANYA COAT_CNV 175 2 -
Final Motifs
Motif 1  width=15
Element Seqn Id St Int Rpt
IAANFDQYTFNSVTL Q66102 144 144 -
IASNFDQYTFNSVVL COAT_TBSVC 148 148 -
LASNFDQYSFNSVVL COAT_TBSVB 148 148 -
IAANFDQYKFNSLRF COAT_CNV 140 140 -
IASNFDQYTFNNVVL P89212 148 148 -
IASNFDQYTFNNVVL Q86586 149 149 -
LASNFDQYMFNTLRL COAT_CRV 144 144 -
IRSNFDQYSFNSVLL COAT_AMCV 148 148 -
LASNFDQYMFNTLRL Q66226 144 144 -
ISANFDQYRFLKVWL O12304 102 102 -
IAASFDQYKFDRVQL Q84832 136 136 -
QAQLYDMYRFTRLRF Q83428 141 141 -
QAQLYDMYRFTRLRF Q83427 141 141 -
QAQLYDMYRFTRLRI COAT_MNSV 141 141 -
VAANWSKYSLLSVRY O72158 109 109 -
VAANWSKYSLLSVRY O72160 109 109 -
IADLYSKYRWLSCEI COAT_TNVA 125 125 -
IADNYSKWRWVSLRI Q88611 126 126 -
VAANWSKYSLLSVTY Q83473 104 104 -
EAANYDMYRLKKLTL COAT_RCNMV 92 92 -
EAANYDMYRMKKLTL Q87030 92 92 -
EAAQYEKYRFTSLRF COAT_TCV 122 122 -
VAQNWSKYAWVAIRY COAT_SBMV 122 122 -
MASQFNKYRLTALRV P89111 120 120 -
EAANYDLYRFAKLRL Q66098 94 94 -
IAASYEKYKFTSLRF Q65990 124 124 -
IADLYSKWRWISCSV O41351 117 117 -
IADLYSKWRWISCSV COAT_TNVD 117 117 -
LATNFNKYRITALTV COAT_CARMV 123 123 -
TAVNYEKYKFRRLSF Q83928 182 182 -
HAVNFSKYSWKYLEF Q83106 99 99 -
LSDLYSKYRWRKLRF Q83942 119 119 -
MAASWGRWKWNSLRF Q83095 94 94 -
LSTGYDMYRLVRCEI Q89761 115 115 -
CSVGYNKYRITDFRI O56987 119 119 -
LLQYYEQYRLLQLNL O15850 740 740 -

Motif 2 width=17
Element Seqn Id St Int Rpt
YVPLCATTETGRVAMYF Q66102 160 1 -
YVPLCSTTEVGRVAIYF COAT_TBSVC 164 1 -
YVPLCGTTEVGRVALYF COAT_TBSVB 164 1 -
YVPLVNTTTNGRVALYF COAT_CNV 156 1 -
YVPLCSTTEVGRVAIYF P89212 164 1 -
YVPLCATTEVGRVAMYF Q86586 165 1 -
YVPMCATTETGRVAIYF COAT_CRV 160 1 -
YVPLCATTEVGRVAMYF COAT_AMCV 164 1 -
YVPMCASTETGRVAIYF Q66226 160 1 -
YAPFCSTTEAGRVGLYF O12304 118 1 -
YVPMCATTETGRVAIYF Q84832 152 1 -
YIPTTGSTSTGRVSILW Q83428 157 1 -
YIPTTGSTSTGRVSILW Q83427 157 1 -
YIPTTGSTSTGRVSLLW COAT_MNSV 157 1 -
YLPSCPSTTSGSIHMGF O72158 125 1 -
YLPSCPSTTSGSIHMGF O72160 125 1 -
YIPKCPTTTSGSIAMAF COAT_TNVA 141 1 -
YSPKCPTTTPGTVAMCL Q88611 142 1 -
YLPSCPSTTSGSIHMGF Q83473 120 1 -
YVPLVTVQNSGRVAMIW COAT_RCNMV 108 1 -
YVPLVTVQNSGRVAMIW Q87030 108 1 -
YSPMSPSTTGGKVALAF COAT_TCV 138 1 -
YLPSCPTTTSGAIHMGF COAT_SBMV 138 1 -
YTSTCSFETSGRVAIAF P89111 136 1 -
YVHDTNATVSGRVSLMW Q66098 110 1 -
YSSTCPTSTGGKVALAF Q65990 140 1 -
YIPKCPTSTQGSVVMAI O41351 133 1 -
YIPKCPTSTQGSVVMAI COAT_TNVD 133 1 -
YSPACSFETNGRVALGF COAT_CARMV 139 1 -
LVPLVSTNYSGRIGVGF Q83928 198 1 -
YIPFVATTFPGQVVLAP Q83106 115 1 -
YLPVCPTSTQGNVSMSL Q83942 135 1 -
YIPAAPSNTQGTVAMGF Q83095 110 1 -
YTPRCAVTTTGSVVLAY Q89761 131 1 -
FSTSCSDTMNGKVAIGF O56987 135 1 -
FIPGCGTTSGGTATLAP O15850 1694 939 -

Motif 3 width=17
Element Seqn Id St Int Rpt
DSEDLEPADRVELANYA Q66102 179 2 -
DSEDPEPADRVELANYS COAT_TBSVC 183 2 -
DSQDPEPADRVELANFG COAT_TBSVB 183 2 -
DSEDPGPDDRAALANYA COAT_CNV 175 2 -
DSEDPEPADRVELANYS P89212 183 2 -
DSEDVEPADRVELANYG Q86586 184 2 -
DSQDLEPVDRIELANMR COAT_CRV 179 2 -
DSEDPEPADRVELANYS COAT_AMCV 183 2 -
DSQDLEPVDRIELANMR Q66226 179 2 -
DSQDPEPTDRVELANFG O12304 137 2 -
DSQDVEPADRDELAIMA Q84832 171 2 -
DSQDPLPIDRAAISSYA Q83428 176 2 -
DSQDPLPIDRAAISSYA Q83427 176 2 -
DSQDPLPIDRAAISSYA COAT_MNSV 176 2 -
DMADTLPVSVNQLSNLR O72158 144 2 -
DMADTLPVSVNQLSNLR O72160 144 2 -
DRNDAAPTARAQLSQSY COAT_TNVA 160 2 -
DRNDVAPGSRVQLSQTY Q88611 161 2 -
DMADTLPVSVNQLSNLR Q83473 139 2 -
DSQDSAPQSRQEISAYS COAT_RCNMV 127 2 -
DSQDSVPQSRQEISAYS Q87030 127 2 -
DAAKPPPNDLASLYNIE COAT_TCV 157 2 -
DMADTLPVSVNQLSNLK COAT_SBMV 157 2 -
DSNDPLPTTKSQLYNFP P89111 155 2 -
DSQDVPPNSRVSIPQCT Q66098 129 2 -
DAANPLPDNLTAFYNLE Q65990 159 2 -
DAQDTVPTTRTQVSQCY O41351 152 2 -
DAQDTVPTTRTQVSQCY COAT_TNVD 152 2 -
DASDTPPTTKVGFYDLG COAT_CARMV 158 2 -
DSSDLVPGNRQEFYALS Q83928 217 2 -
DRSDANPTSIASLEQYD Q83106 134 2 -
DRIDTQPTSITQMQQGY Q83942 154 2 -
DSLDSLPSNLASMSSLD Q83095 129 2 -
DASDVNPDNVTDLLNMA Q89761 150 2 -
DSSDPVPVDKSQLYGMQ O56987 154 2 -
GSFDRLPAHRAEGASGA O15850 1714 3 -