5XWG

Crystal structure of a novel RNA motif that allows for precise positioning of a metal ion

• PDB DOI: https://doi.org/10.2210/pdb5XWG/pdb
• NAKB: 5XWG

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


• Deposited: 2017-06-29 Released: 2017-10-11 
• Deposition Author(s): Kanazawa, H., Kondo, J.
• Funding Organization(s): the Ichiro Kanehara Foundation, AMED, the Japan Science Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 

Literature

Crystal structure of a novel RNA motif that allows for precise positioning of a single metal ion.

Kanazawa, H., Kondo, J.

(2017) J Inorg Biochem 176: 140-143

• PubMed: 28898762 
• DOI: https://doi.org/10.1016/j.jinorgbio.2017.08.029
• Primary Citation of Related Structures:  
  5XWG


• PubMed Abstract: 
  

  We have determined a crystal structure of an RNA duplex containing a novel metal-binding motif. The motif is composed of two sheared G○A base pairs, two unpaired A residues and four phosphate groups in close proximity. Four A residues make an A-A-A-A stacking column at the minor groove side and two G bases are highly inclined, thereby forming the pocket-shaped motif at the major groove side. In the present structure, a hydrated Sr ²⁺ ion exists in the pocket and binds to the O6 and N7 atoms of the two G bases and four phosphate groups. According to the previously-reported metal-binding properties to RNA molecules, many of divalent cations, such as Mg ²⁺ , Mn ²⁺ , Co ²⁺ , Zn ²⁺ , Ba ²⁺ , Pb ²⁺ and Cd ²⁺ , may bind to the motif. This metal-binding motif can be used as a modular building block that allows for precise positioning of a single metal ion in functional nucleic acid molecules.

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Organizational Affiliation: 

Graduate School of Science and Technology, Sophia University, Tokyo 102-8554, Japan.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 5.12 kDa 
• Atom Count: 342 
• Modelled Residue Count: 15 
• Deposited Residue Count: 15 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*GP*CP*UP*(5BU)P*CP*GP*AP*AP*AP*AP*AP*GP*UP*C)-3')	A	15	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SR (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.217 
• R-Value Observed: 0.218 
• Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.544	α = 90
b = 80.544	β = 90
c = 80.544	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Kanazawa, H., Kondo, J.

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Funding Organization	Location	Grant Number
the Ichiro Kanehara Foundation	Japan	--
AMED	Japan	--
the Japan Science Society	Japan	--

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references