2NCI

RNA Bulge Loop that Specifically Binds Metal Ions

PDB DOI: https://doi.org/10.2210/pdb2NCI/pdb
BMRB: 26024
NAKB: 2NCI

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 1.4 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

PubMed: 27631837 Search on PubMedSearch on PubMed Central
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.