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PDBsum entry 2grw
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RNA PDB id
2grw

 

 

 

 

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Contents
DNA/RNA
PDB id:
2grw
Name: RNA
Title: Solution structure of the poliovirus 3'-utr y-stem
Structure: 5'-ggaccucucgaaagagaugucc-3'. Chain: a. Fragment: poliovirus 3'-utr y-stem. Engineered: yes
Source: Synthetic: yes. Other_details: this sequence is a mutant of poliovirus 3'-utr y-stem
NMR struc: 12 models
Authors: H.A.Heus,J.Zoll,M.Tessari,F.J.M.Van Kuppeveld,W.J.G.Melchers
Key ref: J.Zoll et al. (2007). Breaking pseudo-twofold symmetry in the poliovirus 3'-UTR Y-stem by restoring Watson-Crick base pairs. Rna, 13, 781-792. PubMed id: 17449731
Date:
25-Apr-06     Release date:   06-Mar-07    
 Headers
 References

DNA/RNA chain
  G-G-A-C-C-U-C-U-C-G-A-A-A-G-A-G-A-U-G-U-C-C 22 bases

 

 
Rna 13:781-792 (2007)
PubMed id: 17449731  
 
 
Breaking pseudo-twofold symmetry in the poliovirus 3'-UTR Y-stem by restoring Watson-Crick base pairs.
J.Zoll, M.Tessari, F.J.Van Kuppeveld, W.J.Melchers, H.A.Heus.
 
  ABSTRACT  
 
The previously described NMR structure of a 5'-CU-3'/5'-UU-3' motif, which is highly conserved within the 3'-UTR Y-stem of poliovirus-like enteroviruses, revealed striking regularities of the local helix geometry, thus retaining the pseudo-twofold symmetry of the RNA helix. A mutant virus with both pyrimidine base pairs changed into Watson-Crick replicated as wild type, indicating the functional importance of this symmetry relation in viral RNA replication. Here we investigated the effect of changing only one of the two pyrimidine base pairs to Watson-Crick. We determined the NMR structures of two Y-stem variants: one containing the 5'-CU-3'/5'-AU-3' motif, which has been found in wild-type virus isolates as well, and the other containing a 5'-CU-3'/5'-UG-3' motif, which is not present in any enterovirus sequenced to date. Both structures show single pyrimidine mismatches with intercalated bases. In the 5'-CU-3'/5'-AU-3' motif a C-U Watson-Crick-type base pair is formed that retains the pseudo-twofold symmetry, while in the 5'-CU-3'/5'-UG-3' motif a single asymmetric U-U mismatch breaks the twofold symmetry. Surprisingly, for the nonnatural variant no effect of the single base-pair replacement was observed on polioviral RNA replication using an in vitro replicon assay.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20540055 E.Lescrinier, N.Dyubankova, K.Nauwelaerts, R.Jones, and P.Herdewijn (2010).
Structure determination of the top-loop of the conserved 3'-terminal secondary structure in the genome of flaviviruses.
  Chembiochem, 11, 1404-1412.
PDB codes: 2kpc 2kpd
18296482 M.Cevec, C.Thibaudeau, and J.Plavec (2008).
Solution structure of a let-7 miRNA:lin-41 mRNA complex from C. elegans.
  Nucleic Acids Res, 36, 2330-2337.
PDB code: 2jxv
18600227 X.J.Lu, and W.K.Olson (2008).
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.
  Nat Protoc, 3, 1213-1227.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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