2LX1 | pdb_00002lx1

Major Conformation of the Internal Loop 5'GAGU/3'UGAG

• PDB DOI: https://doi.org/10.2210/pdb2LX1/pdb
• BMRB: 18656
• NAKB: 2LX1

• Classification: RNA
• Mutation(s): No 


• Deposited: 2012-08-12 Released: 2012-11-21 
• Deposition Author(s): Kennedy, S.D., Turner, D.H.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 600 
• Conformers Submitted: 19 
• Selection Criteria: structures with the least restraint violations 

Literature

Novel conformation of an RNA structural switch.

Kennedy, S.D., Kierzek, R., Turner, D.H.

(2012) Biochemistry 51: 9257-9259

• PubMed: 23134175 
• DOI: https://doi.org/10.1021/bi301372t
• Primary Citation Related Structures: 
  2LX1


• PubMed Abstract: 
  

  The RNA duplex, (5'GACGAGUGUCA)(2), has two conformations in equilibrium. The nuclear magnetic resonance solution structure reveals that the major conformation of the loop, 5'GAGU/3'UGAG, is novel and contains two unusual Watson-Crick/Hoogsteen GG pairs with G residues in the syn conformation, two A residues stacked on each other in the center of the helix with inverted sugars, and two bulged-out U residues. The structure provides a benchmark for testing approaches for predicting local RNA structure and a sequence that allows the design of a unique arrangement of functional groups and/or a conformational switch into nucleic acids.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.09 kDa 
• Atom Count: 470 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*AP*CP*GP*AP*GP*UP*GP*UP*CP*A)-3')	A, B	11	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 600 
• Conformers Submitted: 19 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Kennedy, S.D., Turner, D.H.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references