5V2R

Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 33 
  • Selection Criteria: structures with the lowest restraint energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Nuclear Magnetic Resonance Structure of an 8 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions.

Kauffmann, A.D.Kennedy, S.D.Zhao, J.Turner, D.H.

(2017) Biochemistry 56: 3733-3744

  • DOI: 10.1021/acs.biochem.7b00201
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The prediction of RNA three-dimensional structure from sequence alone has been a long-standing goal. High-resolution, experimentally determined structures of simple noncanonical pairings and motifs are critical to the development of prediction progra ...

    The prediction of RNA three-dimensional structure from sequence alone has been a long-standing goal. High-resolution, experimentally determined structures of simple noncanonical pairings and motifs are critical to the development of prediction programs. Here, we present the nuclear magnetic resonance structure of the (5'CCAGAAACGGAUGGA) 2 duplex, which contains an 8 × 8 nucleotide internal loop flanked by three Watson-Crick pairs on each side. The loop is comprised of a central 5'AC/3'CA nearest neighbor flanked by two 3RRs motifs, a known stable motif consisting of three consecutive sheared GA pairs. Hydrogen bonding patterns between base pairs in the loop, the all-atom root-mean-square deviation for the loop, and the deformation index were used to compare the structure to automated predictions by MC-sym, RNA FARFAR, and RNAComposer.


    Organizational Affiliation

    Center for RNA Biology, University of Rochester , Rochester, New York 14627, United States.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3')A, B15synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 33 
  • Selection Criteria: structures with the lowest restraint energy 
  • OLDERADO: 5V2R Olderado

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM22939

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-09
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence, Data collection