2L8F | pdb_00002l8f

Structure of a 4X4 Nucleotide RNA Internal Loop from an R2 Retrotransposon

• PDB DOI: https://doi.org/10.2210/pdb2L8F/pdb
• BMRB: 17406
• NAKB: 2L8F

• Classification: RNA
• Mutation(s): No 


• Deposited: 2011-01-11 Released: 2011-08-31 
• Deposition Author(s): Lerman, Y., Kennedy, S.D., Turner, D.H.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 10 
• Selection Criteria: no restraint violations; low constraint energy 

Literature

NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.

Lerman, Y.V., Kennedy, S.D., Shankar, N., Parisien, M., Major, F., Turner, D.H.

(2011) RNA 17: 1664-1677

• PubMed: 21778280 
• DOI: https://doi.org/10.1261/rna.2641911
• Primary Citation Related Structures: 
  2L8F


• PubMed Abstract: 
  

  The NMR solution structure is reported of a duplex, 5'GUGAAGCCCGU/3'UCACAGGAGGC, containing a 4 × 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine-purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37°C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 5'GAA/3'AGG, 5'GAG/3'AGG, 5'GAA/3'AAG, and 5'AAG/3'AGG. The structural information is compared with predictions made with the MC-Sym program.

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Organizational Affiliation: 
• Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.07 kDa 
• Atom Count: 468 
• Modeled Residue Count: 22 
• Deposited Residue Count: 22 
• Unique nucleic acid chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3')	B	11	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 10 
• Selection Criteria: no restraint violations; low constraint energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-31 
Deposition Author(s): Lerman, Y., Kennedy, S.D., Turner, D.H.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references