3P59

First Crystal Structure of a RNA Nanosquare


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Self-assembling RNA square.

Dibrov, S.M.McLean, J.Parsons, J.Hermann, T.

(2011) Proc Natl Acad Sci U S A 108: 6405-6408

  • DOI: 10.1073/pnas.1017999108
  • Primary Citation of Related Structures:  
    3P59

  • PubMed Abstract: 
  • The three-dimensional structures of noncoding RNA molecules reveal recurring architectural motifs that have been exploited for the design of artificial RNA nanomaterials. Programmed assembly of RNA nanoobjects from autonomously folding tetraloop-receptor complexes as well as junction motifs has been achieved previously through sequence-directed hybridization of complex sets of long oligonucleotides ...

    The three-dimensional structures of noncoding RNA molecules reveal recurring architectural motifs that have been exploited for the design of artificial RNA nanomaterials. Programmed assembly of RNA nanoobjects from autonomously folding tetraloop-receptor complexes as well as junction motifs has been achieved previously through sequence-directed hybridization of complex sets of long oligonucleotides. Due to size and complexity, structural characterization of artificial RNA nanoobjects has been limited to low-resolution microscopy studies. Here we present the design, construction, and crystal structure determination at 2.2 Å of the smallest yet square-shaped nanoobject made entirely of double-stranded RNA. The RNA square is comprised of 100 residues and self-assembles from four copies each of two oligonucleotides of 10 and 15 bases length. Despite the high symmetry on the level of secondary structure, the three-dimensional architecture of the square is asymmetric, with all four corners adopting distinct folding patterns. We demonstrate the programmed self-assembly of RNA squares from complex mixtures of corner units and establish a concept to exploit the RNA square as a combinatorial nanoscale platform.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*(5BU)P*G)-3')A, C, E, G15N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(*CP*CP*GP*GP*CP*AP*GP*CP*CP*U)-3')B, D, F, H10N/A
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.18 Å
      • R-Value Free: 0.192 
      • R-Value Work: 0.156 
      • R-Value Observed: 0.157 
      • Space Group: P 31 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 62.378α = 90
      b = 62.378β = 90
      c = 126.268γ = 120
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      PHENIXmodel building
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2011-04-06
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance