5AY4

Crystal structure of RNA duplex containing C-C base pairs obtained in the presence of Hg(II)

• PDB DOI: https://doi.org/10.2210/pdb5AY4/pdb
• NAKB: 5AY4

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2015-08-06 Released: 2015-10-21 
• Deposition Author(s): Kondo, J., Tada, Y., Dairaku, T., Saneyoshi, H., Okamoto, I., Tanaka, Y., Ono, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.196 
• R-Value Work: 0.160 

Starting Model: experimental

Literature

High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like CSilver(I)C Metallo-Base Pairs

Kondo, J., Tada, Y., Dairaku, T., Saneyoshi, H., Okamoto, I., Tanaka, Y., Ono, A.

(2015) Angew Chem Int Ed Engl 54: 13323-13326

• PubMed: 26448329 
• DOI: https://doi.org/10.1002/anie.201507894
• Primary Citation of Related Structures:  
  5AY2, 5AY3, 5AY4


• PubMed Abstract: 
  

  Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices.

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Organizational Affiliation: 

Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554 (Japan). [e-mail].

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 7.72 kDa 
• Atom Count: 659 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3')	A, B	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.196 
• R-Value Work: 0.160 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27	α = 90
b = 44.54	β = 109.1
c = 27.55	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Kondo, J., Tada, Y., Dairaku, T., Saneyoshi, H., Okamoto, I., Tanaka, Y., Ono, A.

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2015-11-11
  Changes: Database references
• Version 1.2: 2017-10-11
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description