5CNR

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

• PDB DOI: https://doi.org/10.2210/pdb5CNR/pdb
• NAKB: 5CNR

• Classification: RNA
• Organism(s): Senecavirus A
• Mutation(s): No 


• Deposited: 2015-07-18 Released: 2016-03-09 
• Deposition Author(s): Boerneke, M., Dibrov, S., Hermann, T.
• Funding Organization(s): UCSD Academic Senate

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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

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

• PubMed: 26914842 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.22 kDa 
• Atom Count: 1,137 
• Modelled Residue Count: 54 
• Deposited Residue Count: 54 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*UP*CP*UP*AP*CP*CP*CP*AP*CP*CP*UP*CP*GP*CP*C)-3')	A, C [auth E]	16	Senecavirus A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*GP*AP*GP*GP*AP*CP*GP*GP*CP*G)-3')	B, D [auth F]	11	Senecavirus A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	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 = 59.934	α = 90
b = 59.934	β = 90
c = 262.622	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Boerneke, M., Dibrov, S., Hermann, T.

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Funding Organization	Location	Grant Number
UCSD Academic Senate	United States	RM069B

Revision History  

• 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