8AMG image
Entry Detail
PDB ID:
8AMG
Keywords:
Title:
Crystal structure of AUGUGGCAU duplex with barium ions (model 1)
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2022-08-03
Release Date:
2022-11-23
Method Details:
Experimental Method:
Resolution:
2.26 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 65 2 2
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
Chain IDs:A, B, C, D, E, F, G, H, I, J, K, L
Chain Length:9
Number of Molecules:12
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.
Rna 29 44 54 (2022)
PMID: 36319090 DOI: 10.1261/rna.079414.122

Abstact

The self-complementary triplet 5'UGG3'/5'UGG3' is a particular structural motif containing noncanonical G-G pair and two U·G wobble pairs. It constitutes a specific structural and electrostatic environment attracting metal ions, particularly Ba2+ ions. Crystallographic research has shown that two Ba2+ cations are located in the major groove of the helix and interact directly with the UGG triplet. A comparison with the unliganded structure has revealed global changes in the RNA structure in the presence of metal ions, whereas thermodynamic measurements have shown increased stability. Moreover, in the structure with Ba2+, an unusual noncanonical G(syn)-G(syn) pair is observed instead of the common G(anti)-G(syn). We further elucidate the metal binding properties of the UGG/UGG triplet by performing crystallographic and thermodynamic studies using DSC and UV melting with other metal ions. The results explain the preferences of the UGG sequence for Ba2+ cations and point to possible applications of this metal-binding propensity.

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