2FDT

Solution structure of a conserved RNA hairpin of eel LINE UnaL2

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 11 
  • Selection Criteria: structures with the lowest energy 

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This is version 1.3 of the entry. See complete history. 


Literature

Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2

Nomura, Y., Kajikawa, M., Baba, S., Nakazato, S., Imai, T., Sakamoto, T., Okada, N., Kawai, G.

(2006) Nucleic Acids Res 34: 5184-5193

  • DOI: 10.1093/nar/gkl664
  • Primary Citation of Related Structures:  
    2FDT

  • PubMed Abstract: 

    • The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3' tail that is critical for their retrotransposition. The predicted secondary structure of the conserved 3' tail of UnaL2 RNA contains a stem region with a putative internal loop ...

    The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3' tail that is critical for their retrotransposition. The predicted secondary structure of the conserved 3' tail of UnaL2 RNA contains a stem region with a putative internal loop. Deletion of the putative internal loop region abolishes UnaL2 mobilization, indicating that this putative internal loop is required for UnaL2 retrotransposition; the exact role of the putative internal loop in retrotransposition, however, has not been elucidated. To establish a structure-based foundation on which to address the issue of the putative internal loop function in retrotransposition, we used NMR to determine the solution structure of a 36 nt RNA derived from the 3' conserved tail of UnaL2. The region forms a compact structure containing a single bulged cytidine and a U-U mismatch. The bulge and mismatch region have conformational flexibility and molecular dynamics simulation indicate that the entire stem of the 3' conserved tail RNA can anisotropically fluctuate at the bulge and mismatch region. Our structural and mutational analyses suggest that stem flexibility contributes to UnaL2 function and that the bulged cytidine and the U-U mismatch are required for efficient retrotransposition.

    Organizational Affiliation: 

    Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
36-merA 36N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 11 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2FDT Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-09
    Changes: Data collection, Database references, Derived calculations