5CNR

Crystal structure-guided design of self-assembling RNA nano triangles


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles.

Boerneke, M.A.Dibrov, S.M.Hermann, T.

(2016) Angew Chem Int Ed Engl 55: 4097-4100

  • DOI: https://doi.org/10.1002/anie.201600233
  • Primary Citation of Related Structures:  
    5CNR

  • PubMed Abstract: 

    RNA nanotechnology uses RNA structural motifs to build nanosized architectures that assemble through selective base-pair interactions. Herein, we report the crystal-structure-guided design of highly stable RNA nanotriangles that self-assemble cooperatively from short oligonucleotides. The crystal structure of an 81 nucleotide nanotriangle determined at 2.6 Å resolution reveals the so-far smallest circularly closed nanoobject made entirely of double-stranded RNA. The assembly of the nanotriangle architecture involved RNA corner motifs that were derived from ligand-responsive RNA switches, which offer the opportunity to control self-assembly and dissociation.


  • Organizational Affiliation

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


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*CP*C)-3')A,
C [auth E]
16Senecavirus A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*AP*GP*AP*GP*GP*AP*CP*GP*GP*CP*G)-3')B,
D [auth F]
11Senecavirus A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.198 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.934α = 90
b = 59.934β = 90
c = 262.622γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UCSD Academic SenateUnited StatesRM069B

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description