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(-) Description

Title :  CRYSTAL STRUCTURE OF P19 COMPLEXED WITH 19-BP SMALL INTERFERING RNA
 
Authors :  K. Ye, L. Malinina, D. J. Patel
Date :  28 Oct 03  (Deposition) - 27 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Protein-Rna Complex, Dimer, Double Helix, Viral Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ye, L. Malinina, D. J. Patel
Recognition Of Small Interfering Rna By A Viral Suppressor Of Rna
Nature V. 426 874 2003
PubMed-ID: 14661029  |  Reference-DOI: 10.1038/NATURE02213
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- R(*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*AP *UP*U)-3'
    Chains: B
    Engineered: YES
    Other Details: 5'-OH AND 3'-OH
    Synthetic: YES
 
Molecule 2 - 5'- R(*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*GP *UP*U)-3'
    Chains: C
    Engineered: YES
    Other Details: 5'-OH AND 3'-OH
    Synthetic: YES
 
Molecule 3 - CORE PROTEIN P19
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 27-158
    Gene: P19
    Mutation: YES
    Organism Scientific: TOMATO BUSHY STUNT VIRUS
    Organism Taxid: 12145

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:28 , PHE A:70 , ARG A:72 , HOH A:168 , HOH A:208BINDING SITE FOR RESIDUE SO4 A 159
2AC2SOFTWARESER A:38 , THR A:40 , HIS A:84 , HOH A:167 , HOH A:174BINDING SITE FOR RESIDUE SO4 A 160

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R9F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R9F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R9F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R9F)

(-) Exons   (0, 0)

(no "Exon" information available for 1R9F)

(-) 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:121
 aligned with P19_TBSVC | P11690 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:124
                                    34        44        54        64        74        84        94       104       114       124       134       144    
            P19_TBSVC    25 GTTSPFKLPDESPSWTEWRLHNDETNSNQDNPLGFKESWGFGKVVFKRYLRYDRTEASLHRVLGSWTGDSVNYAASRFFGFDQIGCTYSIRFRGVSITVSGGSRTLQHLCEMAIRSKQELLQLA 148
               SCOP domains d1r9fa_ A: Tombusvirus P1   9 core protein, VP19                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Tombus_P19-1r9fA01 A:27   -148                                                                                             Pfam domains
         Sec.struct. author .............hhhhhhhhhhhh---.....eeeeeeee..eeeeeeee...hhhhhhhhhh..hhhhhhhhhhh.......eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r9f A  25 HmTSPFKLPDESPSWTEWRLHNDET---QDNPLGFKESWGFGKVVFKRYLRYDRTEASLHRVLGSWTGDSVNYAASRFFGFDQIGCTYSIRFRGVSITVSGGSRTLQHLCEmAIRSKQEmLQmA 148
                             |      34        44    |   54        64        74        84        94       104       114       124       134 |     144  | 
                             |                     49  53                                                                                136-MSE 144-MSE
                            26-MSE                                                                                                                  147-MSE


Chain B from PDB  Type:DNA/RNA  Length:20
                                                    
                 1r9f B   1 CGUACGCGGAAUACUUCGAU  20
                                    10        20


Chain C from PDB  Type:DNA/RNA  Length:20
                                                    
                 1r9f C   1 UCGAAGUAUUCCGCGUACGU  20
                                    10        20
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R9F)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (P19_TBSVC | P11690)
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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  1r9f
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