2NCI

RNA Bulge Loop that Specifically Binds Metal Ions

  • Classification: RNA
  • Mutation(s): No 

  • Deposited: 2016-04-01 Released: 2016-09-28 
  • Deposition Author(s): Gu, X., Schroeder, S.J.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions.

Gu, X.Park, S.Y.Tonelli, M.Cornilescu, G.Xia, T.Zhong, D.Schroeder, S.J.

(2016) J Phys Chem Lett 7: 3841-3846

  • DOI: https://doi.org/10.1021/acs.jpclett.6b01465
  • Primary Citation of Related Structures:  
    2NCI

  • PubMed Abstract: 

    Metal ions are critical for RNA structure and enzymatic activity. We present the structure of an asymmetric RNA loop that binds metal ions and has an essential function in a bacteriophage packaging motor. Prohead RNA is a noncoding RNA that is required for genome packaging activity in phi29-like bacteriophage. The loops in GA1 and phi29 bacteriophage share a conserved adenine that forms a base triple, although the structural context for the base triple differs. NMR relaxation studies and femtosecond time-resolved fluorescence spectroscopy reveal the dynamic behavior of the loop in the metal ion bound and unbound forms. The mechanism of metal ion binding appears to be an induced conformational change between two dynamic ensembles rather than a conformational capture mechanism. These results provide experimental benchmarks for computational models of RNA-metal ion interactions.


  • Organizational Affiliation

    Department of Chemistry & Biochemistry and Department of Microbiology & Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (28-MER)28N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-05
    Changes: Database references
  • Version 1.2: 2016-10-12
    Changes: Database references
  • Version 1.3: 2016-10-19
    Changes: Database references