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(-) Description

Title :  CRYSTAL STRUCTURE OF TAV2B/SIRNA COMPLEX
 
Authors :  Y. A. Yuan, H. -Y. Chen
Date :  12 Feb 08  (Deposition) - 22 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.82
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B,C,D  (2x)
Keywords :  Rnai Suppression, Nucleus, Suppressor Of Rna Silencing, Gene Regulation-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. -Y. Chen, J. Yang, C. Lin, Y. A. Yuan
Structural Basis For Rna-Silencing Suppression By Tomato Aspermy Virus Protein 2B
Embo Rep. V. 9 754 2008
PubMed-ID: 18600235  |  Reference-DOI: 10.1038/EMBOR.2008.118

(-) Compounds

Molecule 1 - PROTEIN 2B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-69
    Gene: RNA4A
    Organism Common: TAV
    Organism Scientific: TOMATO ASPERMY VIRUS
    Organism Taxid: 12315
    Synonym: TAV2B
 
Molecule 2 - RNA (5'- D(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)- 3')
    Chains: C, D
    Engineered: YES
    Synonym: SIRNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2ZI0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZI0)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2ZI0)

(-) 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:60
 aligned with 2B_TAV | Q8UYT3 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:60
                                    14        24        34        44        54        64
                2B_TAV    5 EIPLHEIIRKLERMNQKKQAQRKRHKLNRKERGHKSPSEQRRSELWHARQVELSAINSDN 64
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  2zi0 A  5 EIPLHEIIRKLERmNQKKQAQRKRHKLNRKERGHKSPSEQRRSELWHARQVELSAINSDN 64
                                    14   |    24        34        44        54        64
                                        18-MSE                                          


Chain B from PDB  Type:PROTEIN  Length:55
 aligned with 2B_TAV | Q8UYT3 from UniProtKB/Swiss-Prot  Length:95

    Alignment length:55
                                    13        23        33        43        53     
                2B_TAV    4 IEIPLHEIIRKLERMNQKKQAQRKRHKLNRKERGHKSPSEQRRSELWHARQVELS 58
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
           Pfam domains (1) -Cucumo_2B-2zi0B01 B:5-58                               Pfam domains (1)
           Pfam domains (2) -Cucumo_2B-2zi0B02 B:5-58                               Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  2zi0 B  4 IEIPLHEIIRKLERmNQKKQAQRKRHKLNRKERGHKSPSEQRRSELWHARQVELS 58
                                    13    |   23        33        43        53     
                                         18-MSE                                    


Chain C from PDB  Type:DNA/RNA  Length:20
                                                   
                  2zi0 C  1 AGACAGCAUUAUGCUGUCUU 20
                                    10        20


Chain D from PDB  Type:DNA/RNA  Length:20
                                                   
                  2zi0 D  1 AGACAGCAUUAUGCUGUCUU 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  (0, 0)

(no "SCOP Domain" information available for 2ZI0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZI0)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Cucumo_2B] (1)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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

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        2B_TAV | Q8UYT3: 3cz3

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