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(-) Description

Title :  STRUCTURE OF TRIATOMA VIRUS (TRV)
 
Authors :  G. Squires, J. Pous
Date :  02 Jun 10  (Deposition) - 28 Jul 10  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (60x)
Keywords :  Insect Cripavirus, Icosahedral Virus, Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Squires, J. Pous, G. S. Rozas-Dennis, M. D. Costabel, J. Agirre, G. Marti, J. Navaza, D. M. A. Guerin, F. A. Rey
The Crystallographic Structure Of Triatoma Virus (Trv) Highlights The Dicistroviridae And Picornaviridae Family Differences
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A
    Fragment: VP1 (UNP RESIDUES 598-868)
    Organism Scientific: TRIATOMA VIRUS
    Organism Taxid: 103442
 
Molecule 2 - CAPSID PROTEIN
    Chains: B
    Fragment: VP2 (UNP RESIDUES 1-255)
    Organism Scientific: TRIATOMA VIRUS
    Organism Taxid: 103442
 
Molecule 3 - CAPSID PROTEIN
    Chains: C
    Fragment: VP3 (UNP RESIDUES 313-597)
    Organism Scientific: TRIATOMA VIRUS
    Organism Taxid: 103442

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (60x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3NAP)

(-) Sites  (0, 0)

(no "Site" information available for 3NAP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NAP)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu B:110 -Pro B:111
2Thr C:44 -Pro C:45
3Arg C:200 -Pro C:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NAP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NAP)

(-) Exons   (0, 0)

(no "Exon" information available for 3NAP)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:264
 aligned with Q9QEY5_9VIRU | Q9QEY5 from UniProtKB/TrEMBL  Length:868

    Alignment length:264
                                   607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857    
         Q9QEY5_9VIRU   598 VGFASAGTRDIRSSYVEGKFIPQDITGMSRNHELDEQPSQECIGERILSFSELIKRNSWRYVSDEKSLIYPAYAFDNPAAMYTAADKLPVWTLTPRSGFPTLLTSIGAMYAFYRGGIRLKIVPGVADQPKPLVEVALFTMQDQGYIIKANDYSTDFCSSNIYENFVTKGIAEVQTPYYSRVNTSVVSAPVLYNAGNISPLMPNVMYKITSNSSNILLGHSAADDFRFGFLLGAPLAISATALRDNFTGSSATVSLPTFSNFYLS 861
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------------------CRPV_capsid-3napA01 A:36-241                                                                                                                                                                                  ----------------------- Pfam domains
         Sec.struct. author ...ee.....hhhhhhh..........hhhhhh..hhhhhhhh.....hhhhhh...eeeeee...eeee........eeee........eeee......hhhhhhhh.eeeee..eeeeeee........eeeeeee.........ee..........eeeee......eeeee........ee...................eeeeee....eeeeeee....eeeee.....eee.hhhhh............hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nap A   1 VGFASAGTRDIRSSYVEGKFIPQDITGMSRNHELDEQPSQECIGERILSFSELIKRNSWRYVSDEKSLIYPAYAFDNPAAMYTAADKLPVWTLTPRSGFPTLLTSIGAMYAFYRGGIRLKIVPGVADQPKPLVEVALFTMQDQGYIIKANDYSTDFCSSNIYENFVTKGIAEVQTPYYSRVNTSVVSAPVLYNAGNISPLMPNVMYKITSNSSNILLGHSAADDFRFGFLLGAPLAISATALRDNFTGSSATVSLPTFSNFYLS 264
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with Q9QEY5_9VIRU | Q9QEY5 from UniProtKB/TrEMBL  Length:868

    Alignment length:247
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       
         Q9QEY5_9VIRU     9 KQMNVNSSQDTTFEQRSQEKVQAGEINESIEFRNQITTFVHDNPIITEQLIGDSPQPSGDVRSVSDARTHSIIDFLERPQFIGSFLWNTSDIENKEIFSLKLPDALMSPMIREKLSGFTSFSASTVFHIQVNAHPFQCGRLVLAAVPVPDILPLHRLNMLSFDVSNVITLPHVQLDISKETEVLLKIPYVSPFVQYDLVTKFTPWAAFLAHVYAPLNTPSAASLQVNVFAHFEDIKLGFPTSAIVAQ 255
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..hhhhhh...........eeeee..eeeee...............hhhhhh........hhhhhhh..eeeeeeeee.......eeeeeeehhhhhhhhhhhhhh...eeeeeeeeeeee......eeeeeeeeee.....hhhhhhhhhhhhhhhhh..eeeee.....eeeeee........ee........eeeeeeeeeeee.....eeeeeeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nap B   9 KQMNVNSSQDTTFEQRSQEKVQAGEINESIEFRNQITTFVHDNPIITEQLIGDSPQPSGDVRSVSDARTHSIIDFLERPQFIGSFLWNTSDIENKEIFSLKLPDALMSPMIREKLSGFTSFSASTVFHIQVNAHPFQCGRLVLAAVPVPDILPLHRLNMLSFDVSNVITLPHVQLDISKETEVLLKIPYVSPFVQYDLVTKFTPWAAFLAHVYAPLNTPSAASLQVNVFAHFEDIKLGFPTSAIVAQ 255
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       


Chain C from PDB  Type:PROTEIN  Length:276
 aligned with Q9QEY5_9VIRU | Q9QEY5 from UniProtKB/TrEMBL  Length:868

    Alignment length:276
                                   322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582      
         Q9QEY5_9VIRU   313 SKPLTTIPPTIVVQRPSQYFNNADGVDQGLPLSLKYGNEVILKTPFAGTSSDEVALEYVLKIPNYFSRFKYSSTSLPKQVLWTSPVHPQIIRNHVTVVDAPGQPTLLAYATGFFKYWRGGLVYTFRFVKTNYHSGRVQITFHPFVGYDDVMDSDGKIVRDEYVYRVVVDLRDQTEATLVVPFTSLTPYKVCADVFNSANRPKYNYEPRDFKVYDNTTDQFFTGTLCVSALTPLVSSSAVVSSTIDVLVEVKASDDFEVAVPNTPLWLPVDSLTERP 588
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------------------------------------------Rhv-3napC01 C:55-220                                                                                                                                                  -------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------Rhv-3napC02 C:55-220                                                                                                                                                  -------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .............................ee.......................hhhhhh...eeeeeeeee.......eeeeee.....ee..........eehhhhhhhh.eeeee..eeeeeeee......eeeeeeeee..hhhhh........hhhhh.eeeeee....eeeeee........ee....ee........ee................eeeeeee.............eeeeeeeeee....eeeee....eee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nap C   1 SKPLTTIPPTIVVQRPSQYFNNADGVDQGLPLSLKYGNEVILKTPFAGTSSDEMALEYVLKIPNYFSRFKYSSTSLPKQVLWTSPVHPQIIRNHVTVVDAPGQPTLLAYATGFFKYWRGGLVYTFRFVKTNYHSGRVQITFHPFVGYDDVMDSDGKIVRDEYVYRVVVDLRDQTEATLVVPFTSLTPYKVCADVFNSANRPKYNYEPRDFKVYDNTTDQFFTGTLCVSALTPLVSSSAVVSSTIDVLVEVKASDDFEVAVPNTPLWLPVDSLTERP 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3NAP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NAP)

(-) Pfam Domains  (2, 3)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9QEY5_9VIRU | Q9QEY5)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  Cis Peptide Bonds
    Arg C:200 - Pro C:201   [ RasMol ]  
    Leu B:110 - Pro B:111   [ RasMol ]  
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 Related Entries

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UniProtKB/TrEMBL
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