4JRT

Crystal structure of an A-form RNA duplex containing three GU base pairs

• PDB DOI: https://doi.org/10.2210/pdb4JRT/pdb
• NAKB: 4JRT

• Classification: RNA
• Mutation(s): No 


• Deposited: 2013-03-21 Released: 2013-06-05 
• Deposition Author(s): Kondo, J., Dock-Bregeon, A.C., Willkomm, D.K., Hartmann, R.K., Westhof, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.228 
• R-Value Work: 0.185 

Literature

Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet

Kondo, J., Dock-Bregeon, A.C., Willkomm, D.K., Hartmann, R.K., Westhof, E.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 634-639

• PubMed: 23722840 
• DOI: https://doi.org/10.1107/S1744309113013018
• Primary Citation of Related Structures:  
  4JRT


• PubMed Abstract: 
  

  In the course of a crystallographic study of a 132 nt variant of Aquifex aeolicus 6S RNA, a crystal structure of an A-form RNA duplex containing 12 base pairs was solved at a resolution of 2.6 Å. In fact, the RNA duplex is part of the 6S RNA and was obtained by accidental but precise degradation of the 6S RNA in a crystallization droplet. 6S RNA degradation was confirmed by microscopic observation of crystals and gel electrophoresis of crystallization droplets. The RNA oligomers obtained form regular A-form duplexes containing three GoU wobble-type base pairs, one of which engages in intermolecular contacts through a ribose-zipper motif at the crystal-packing interface.

---

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: 7.7 kDa 
• Atom Count: 540 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*GP*GP*UP*GP*GP*UP*GP*CP*GP*GP*G)-3')	A	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*CP*UP*GP*CP*AP*CP*UP*GP*CP*CP*C)-3')	B	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.228 
• R-Value Work: 0.185 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.33	α = 90
b = 29.33	β = 90
c = 89.76	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-05 
Deposition Author(s): Kondo, J., Dock-Bregeon, A.C., Willkomm, D.K., Hartmann, R.K., Westhof, E.

Revision History  

• Version 1.0: 2013-06-05
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description