3P59

First Crystal Structure of a RNA Nanosquare


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1793 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.156 

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.USA 108: 6405-6408

  • DOI: 10.1073/pnas.1017999108

  • 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-rece ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
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
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*GP*GP*CP*AP*GP*CP*CP*U)-3')B,D,F,H10N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCO
Query on NCO

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5BU
Query on 5BU
A, C, E, G
RNA LINKINGC9 H12 Br N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1793 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.156 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 62.378α = 90.00
b = 62.378β = 90.00
c = 126.268γ = 120.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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