WORKLIST ENTRIES (1):
ICOSAHEDRAL View alignment View Structure Icosahedral viral capsid protein signature
Type of fingerprint: COMPOUND with 3 elements
Links:
PRINTS; PR00235 HSVCAPSIDMCP; PR00236 HSVCAPSIDP40; PR00865 HPVCAPSIDL1
INTERPRO; IPR000937
PROSITE; PS00555 ICOSAH_VIR_COAT_S
PFAM; PF00729 Viral_coat
PDB; 2TBV 3Dinfo
SCOP; 2TBV
CATH; 2TBV
Creation date 11-MAR-1995; UPDATE 27-JUN-1999
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).
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 FINGERPRINT INDEX
3| 36 36 36
2| 0 0 0
--+----------------
| 1 2 3
True positives..
Q66102 COAT_TBSVC COAT_TBSVB COAT_CNV
P89212 Q86586 COAT_CRV COAT_AMCV
Q66226 O12304 Q84832 Q83428
Q83427 COAT_MNSV O72158 O72160
COAT_TNVA Q88611 Q83473 COAT_RCNMV
Q87030 COAT_TCV COAT_SBMV P89111
Q66098 Q65990 O41351 COAT_TNVD
COAT_CARMV Q83928 Q83106 Q83942
Q83095 Q89761 O56987 O15850
PROTEIN TITLES
Q66102 CAPSID PROTEIN - CARNATION ITALIAN RINGSPOT VIRUS.
COAT_TBSVC COAT PROTEIN (P41 CAPSID PROTEIN) - TOMATO BUSHY STUNT VIRUS
COAT_TBSVB COAT PROTEIN - TOMATO BUSHY STUNT VIRUS (STRAIN BS-3) (TBSV)
COAT_CNV COAT PROTEIN - CUCUMBER NECROSIS VIRUS (CNV).
P89212 41K PROTEIN - TOMATO BUSHY STUNT VIRUS.
Q86586 COAT PROTEIN - PELARGONIUM LEAF CURL VIRUS.
COAT_CRV COAT PROTEIN - CYMBIDIUM RINGSPOT VIRUS.
COAT_AMCV COAT PROTEIN - ARTICHOKE MOTTLED CRINKLE VIRUS (AMCV).
Q66226 TRANSLATED REGION - CYMBIDIUM RINGSPOT VIRUS.
O12304 CAPSID PROTEIN - GALINSOGA MOSAIC CARMOVIRUS.
Q84832 CAPSID PROTEIN - POTHOS LATENT VIRUS.
Q83428 COAT PROTEIN - MELON NECROTIC SPOT VIRUS (MNSV).
Q83427 COAT PROTEIN - MELON NECROTIC SPOT VIRUS (MNSV).
COAT_MNSV COAT PROTEIN - MELON NECROTIC SPOT VIRUS (MNSV).
O72158 COAT PROTEIN - SOUTHERN BEAN MOSAIC VIRUS (SBMV).
O72160 COAT PROTEIN - SOUTHERN BEAN MOSAIC VIRUS (SBMV).
COAT_TNVA COAT PROTEIN - TOBACCO NECROSIS VIRUS (STRAIN A) (TNV).
Q88611 COAT PROTEIN - TOBACCO NECROSIS VIRUS.
Q83473 COAT PROTEIN - SOUTHERN BEAN MOSAIC VIRUS (SBMV).
COAT_RCNMV COAT PROTEIN (CAPSID PROTEIN) - RED CLOVER NECROTIC MOSAIC V
Q87030 UNIDENTIFIED GENES, THREE COMPLETE CDS'S INCLUDING FUSION PR
COAT_TCV COAT PROTEIN - TURNIP CRINKLE VIRUS (TCV).
COAT_SBMV COAT PROTEIN PRECURSOR (CAPSID PROTEIN) - SOUTHERN BEAN MOSA
P89111 CAPSID PROTEIN - SAGUARO CACTUS VIRUS.
Q66098 P37K PROTEIN - CARNATION RINGSPOT VIRUS.
Q65990 COAT PROTEIN - CARDAMINE CHLOROTIC FLECK VIRUS.
O41351 29 KDA COAT PROTEIN - TOBACCO NECROSIS VIRUS.
COAT_TNVD COAT PROTEIN - TOBACCO NECROSIS VIRUS (STRAIN D) (TNV).
COAT_CARMV COAT PROTEIN - CARNATION MOTTLE VIRUS (CARMV).
Q83928 COAT PROTEIN (P48) - UNIDENTIFIED.
Q83106 CAPSID PROTEIN - LEEK WHITE STRIPE VIRUS.
Q83942 CAPSID PROTEIN - OLIVE LATENT VIRUS 1.
Q83095 VIRAL COAT PROTEIN - LUCERNE TRANSIENT STREAK VIRUS.
Q89761 CAPSID - COWPEA MOTTLE VIRUS.
O56987 COAT PROTEIN - PELARGONIUM FLOWER BREAK VIRUS.
O15850 L3162.1 PROTEIN - LEISHMANIA MAJOR.
SCAN HISTORY
OWL25_2 2 150 NSINGLE
SPTR37_9f 4 100 NSINGLE
INITIAL MOTIF SETS
ICOSAHEDRAL1 Length of motif = 15 Motif number = 1
Icosahedral viral capsid protein motif I - 1
PCODE ST INT
LASNFDQYSFNSVVL COAT_TBSVB 148 148
LASNFDQYSFNSVVL NRL_2TBVA1 47 47
LASNFDQYSFNSVVL NRL_2TBVB 47 47
IASNFDQYTFNSVVL COAT_TBSVC 148 148
IAANFDQYKFNSLRF COAT_CNV 140 140
LASNFDQYMFNTLRL COAT_CRV 144 144
VAQNWSKYAWVAIRY COAT_SBMV 122 122
EAAQYEKYRFTSLRF COAT_TCV 122 122
QAQLYDMYRFTRLRI COAT_MNSV 141 141
LATNFNKYRITALTV COAT_CARMV 123 123
QSQMWNTIVFNSVRI COAT_MCMV 94 94
ICOSAHEDRAL2 Length of motif = 17 Motif number = 2
Icosahedral viral capsid protein motif II - 1
PCODE ST INT
YVPLCGTTEVGRVALYF COAT_TBSVB 164 1
YVPLCGTTEVGRVALYF NRL_2TBVA1 63 1
YVPLCGTTEVGRVALYF NRL_2TBVB 63 1
YVPLCSTTEVGRVAIYF COAT_TBSVC 164 1
YVPLVNTTTNGRVALYF COAT_CNV 156 1
YVPMCATTETGRVAIYF COAT_CRV 160 1
YLPSCPTTTSGAIHMGF COAT_SBMV 138 1
YSPMSPSTTGGKVALAF COAT_TCV 138 1
YIPTTGSTSTGRVSLLW COAT_MNSV 157 1
YSPACSFETNGRVALGF COAT_CARMV 139 1
WETFTADTTSGYISMAF COAT_MCMV 110 1
ICOSAHEDRAL3 Length of motif = 17 Motif number = 3
Icosahedral viral capsid protein motif III - 1
PCODE ST INT
DSQDPEPADRVELANFG COAT_TBSVB 183 2
DSQDPEPADRVELANFG NRL_2TBVA1 82 2
DSQDPEPADRVELANFG NRL_2TBVB 82 2
DSEDPEPADRVELANYS COAT_TBSVC 183 2
DSEDPGPDDRAALANYA COAT_CNV 175 2
DSQDLEPVDRIELANMR COAT_CRV 179 2
DMADTLPVSVNQLSNLK COAT_SBMV 157 2
DAAKPPPNDLASLYNIE COAT_TCV 157 2
DSQDPLPIDRAAISSYA COAT_MNSV 176 2
DASDTPPTTKVGFYDLG COAT_CARMV 158 2
DYMLSIPTGVEDVARIV COAT_MCMV 129 2
FINAL MOTIF SETS
ICOSAHEDRAL1 Length of motif = 15 Motif number = 1
Icosahedral viral capsid protein motif I - 4
PCODE ST INT
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
ICOSAHEDRAL2 Length of motif = 17 Motif number = 2
Icosahedral viral capsid protein motif II - 4
PCODE ST INT
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
ICOSAHEDRAL3 Length of motif = 17 Motif number = 3
Icosahedral viral capsid protein motif III - 4
PCODE ST INT
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
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