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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