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(-) Description

Title :  CRYSTAL STRUCTURE OF CIRV P19 BOUND TO SIRNA
 
Authors :  J. M. Vargason, G. Szittya, J. Burgyan, T. M. T. Hall
Date :  03 Dec 03  (Deposition) - 13 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rnai, Protein-Rna Complex, Rna Double Helix, Rna Length Recognition, Rna Binding Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Vargason, G. Szittya, J. Burgyan, T. M. T. Hall
Size Selective Recognition Of Sirna By An Rna Silencing Suppressor
Cell(Cambridge, Mass. ) V. 115 799 2003
PubMed-ID: 14697199  |  Reference-DOI: 10.1016/S0092-8674(03)00984-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- R(P*CP*GP*UP*AP*CP*GP*CP*GP*UP*CP*AP*CP*GP*CP*GP*UP*AP*CP*G P*UP*U)-3'
    Chains: C, D
    Engineered: YES
    Other Details: SYNTHESIZED BY DHARMACON
    Synthetic: YES
 
Molecule 2 - 19 KDA PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX2T
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: P19
    Organism Scientific: CARNATION ITALIAN RINGSPOT VIRUS
    Organism Taxid: 39443

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1RPU)

(-) Sites  (0, 0)

(no "Site" information available for 1RPU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RPU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RPU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RPU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RPU)

(-) Exons   (0, 0)

(no "Exon" information available for 1RPU)

(-) Sequences/Alignments

Asymmetric/Biological 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:139
 aligned with P19_CIRV | Q66104 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:145
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147     
             P19_CIRV     8 NDTREQANGERWDGGSGGITSPFKLPDESPSWTEWRLYNDETNSNQDNPLGFKESWGFGKVVFKRYLRYDRTEASLHRVLGSWTGDSVNYAASRFLGANQVGCTYSIRFRGVSVTISGGSRTLQHLCEMAIRSKQELLQLTPVEV 152
               SCOP domains d1rpua_ A: Tombusvirus P19 core protein,       VP19                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...................hhhhhhhhh..------...eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rpu A   8 NDTREQANGERWDGGSGGITSPFKLPDESPSWTEWRLYNDE------NPLGFKESWGFGKVVFKRYLRYDRTEASLHRVLGSWTGDSVNYAASRFLGANQVGCTYSIRFRGVSVTISGGSRTLQHLCEMAIRSKQELLQLTPVEV 152
                                    17        27        37        47|      |57        67        77        87        97       107       117       127       137       147     
                                                                   48     55                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:136
 aligned with P19_CIRV | Q66104 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:142
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147  
             P19_CIRV     8 NDTREQANGERWDGGSGGITSPFKLPDESPSWTEWRLYNDETNSNQDNPLGFKESWGFGKVVFKRYLRYDRTEASLHRVLGSWTGDSVNYAASRFLGANQVGCTYSIRFRGVSVTISGGSRTLQHLCEMAIRSKQELLQLTP 149
               SCOP domains d1rpub_ B: Tombusvirus P19 core protein,       VP19                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Tombus_P19-1rpuB01 B:8-149                                                                                                                     Pfam domains (1)
           Pfam domains (2) Tombus_P19-1rpuB02 B:8-149                                                                                                                     Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh...................hhhhhhhhh..------...eeeeeeee..eeeeeeee...hhhhhhhhh...hhhhhhhhhhh.......eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rpu B   8 NDTREQANGERWDGGSGGITSPFKLPDESPSWTEWRLYNDE------NPLGFKESWGFGKVVFKRYLRYDRTEASLHRVLGSWTGDSVNYAASRFLGANQVGCTYSIRFRGVSVTISGGSRTLQHLCEMAIRSKQELLQLTP 149
                                    17        27        37        47|      |57        67        77        87        97       107       117       127       137       147  
                                                                   48     55                                                                                              


Chain C from PDB  Type:RNA  Length:21
                                                     
                 1rpu C   1 CGUACGCGUCACGCGUACGUU  21
                                    10        20 


Chain D from PDB  Type:RNA  Length:21
                                                     
                 1rpu D   1 CGUACGCGUCACGCGUACGUU  21
                                    10        20
   Legend:   → Mismatch (orange background)
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  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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1RPU)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Tombus_P19] (2)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P19_CIRV | Q66104)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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