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(-) Description

Title :  CRYSTAL STRUCTURE OF TOMATO ASPERMY VIRUS 2B IN COMPLEX WITH SIRNA
 
Authors :  J. B. Ma, F. Li, S. W. Ding, D. J. Patel
Date :  27 Apr 08  (Deposition) - 05 May 09  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.23
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Protein-Dsrna Complex, Coiled Coil, Nucleus, Suppressor Of Rna Silencing, Viral Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Ma, F. Li, S. W. Ding, D. J. Patel
Structural Basis For Sirna Recognition By 2B, A Viral Suppressor Of Non-Cell Autonomous Rna Silencing
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN 2B
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-GOLD(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: TAV2B N69
    Gene: RNA2
    Organism Common: TAV
    Organism Scientific: TOMATO ASPERMY VIRUS
    Organism Taxid: 12315
 
Molecule 2 - RNA (5'- R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*A )-3')
    Chains: E, G
    Engineered: YES
    Fragment: PPI-1
    Synthetic: YES
 
Molecule 3 - RNA (5'- R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*G )-3')
    Chains: F, H
    Engineered: YES
    Fragment: PPI-2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3CZ3)

(-) Sites  (0, 0)

(no "Site" information available for 3CZ3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CZ3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CZ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CZ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CZ3)

(-) Exons   (0, 0)

(no "Exon" information available for 3CZ3)

(-) 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:56
 aligned with 2B_TAV | Q8UYT3 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:56
                                    12        22        32        42        52      
                2B_TAV    3 SIEIPLHEIIRKLERMNQKKQAQRKRHKLNRKERGHKSPSEQRRSELWHARQVELS 58
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  3cz3 A  3 SIEIPLHEIIRKLERMNQKKQAQRKRHKLNRKERGHKSPSEQRRSELWHARQVELS 58
                                    12        22        32        42        52      


Chain B from PDB  Type:PROTEIN  Length:56
 aligned with 2B_TAV | Q8UYT3 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:56
                                    12        22        32        42        52      
                2B_TAV    3 SIEIPLHEIIRKLERMNQKKQAQRKRHKLNRKERGHKSPSEQRRSELWHARQVELS 58
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  3cz3 B  3 SIEIPLHEIIRKLERMNQKKQAQRKRHKLNRKERGHKSPSEQRRSELWHARQVELS 58
                                    12        22        32        42        52      


Chain C from PDB  Type:PROTEIN  Length:54
 aligned with 2B_TAV | Q8UYT3 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:54
                                    14        24        34        44        54    
                2B_TAV    5 EIPLHEIIRKLERMNQKKQAQRKRHKLNRKERGHKSPSEQRRSELWHARQVELS 58
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                  3cz3 C  5 EIPLHEIIRKLERMNQKKQAQRKRHKLNRKERGHKSPSEQRRSELWHARQVELS 58
                                    14        24        34        44        54    


Chain D from PDB  Type:PROTEIN  Length:56
 aligned with 2B_TAV | Q8UYT3 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:56
                                    12        22        32        42        52      
                2B_TAV    3 SIEIPLHEIIRKLERMNQKKQAQRKRHKLNRKERGHKSPSEQRRSELWHARQVELS 58
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  3cz3 D  3 SIEIPLHEIIRKLERMNQKKQAQRKRHKLNRKERGHKSPSEQRRSELWHARQVELS 58
                                    12        22        32        42        52      


Chain E from PDB  Type:RNA  Length:19
                                                  
                  3cz3 E  1 CGUACGCGGAAUACUUCGA 19
                                    10         


Chain F from PDB  Type:RNA  Length:19
                                                  
                  3cz3 F  1 UCGAAGUAUUCCGCGUACG 19
                                    10         


Chain G from PDB  Type:RNA  Length:19
                                                  
                  3cz3 G  1 CGUACGCGGAAUACUUCGA 19
                                    10         


Chain H from PDB  Type:RNA  Length:19
                                                  
                  3cz3 H  1 UCGAAGUAUUCCGCGUACG 19
                                    10
   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  (0, 0)

(no "SCOP Domain" information available for 3CZ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3CZ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CZ3)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (2B_TAV | Q8UYT3)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
cellular component
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        2B_TAV | Q8UYT3: 2zi0

(-) Related Entries Specified in the PDB File

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