8AMK

Crystal structure of AUGUGGCAU duplex crystallized in the presence of calcium ions

Summary for 8AMK

• Entry DOI: 10.2210/pdb8amk/pdb
• Related: 8AMG 8AMI 8AMJ
• Descriptor: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3') (2 entities in total)
• Functional Keywords: ug wobble, ca ions, rna, ugg repeats
• Biological source: Homo sapiens
• Total number of polymer chains: 28
• Total formula weight: 80437.03

Authors

Kiliszek, A.,Rypniewski, W. (deposition date: 2022-08-03, release date: 2022-11-23, Last modification date: 2024-02-07)

Primary citation

Kiliszek, A.,Pluta, M.,Bejger, M.,Rypniewski, W.
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

PubMed Abstract: 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.

PubMed: 36319090
DOI: 10.1261/rna.079414.122

Experimental method

X-RAY DIFFRACTION (2.85 Å)