ISDA

Deposition Date 2017-12-14

Release Date 2018-10-17

Last Version Date 2024-03-27

Entry Detail

PDB ID:

5YZE

Keywords:

ANTIBIOTICS/DNA

Title:

Crystal structure of the [Co2+-(chromomycin A3)2]-d(CCG)3 complex

Biological Source:

Source Organism:

synthetic construct (Taxon ID: 32630)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.87 Å

R-Value Free:

0.25

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

P 32 1 2

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')
Chain IDs:A, B
Chain Length:11
Number of Molecules:2
Biological Source:synthetic construct

Ligand Molecules

CPH

Primary Citation

CoII(Chromomycin)2 Complex Induces a Conformational Change of CCG Repeats from i-Motif to Base-Extruded DNA Duplex

Chen, Y.W, Satange, R, Wu, P.C, Jhan, C.R, Chang, C.K, Chung, K.R, Waring, M.J, Lin, S.W, Hsieh, L.C, Hou, M.H.Show

Int J Mol Sci 19 ? ? (2018)

PMID: 30227633 DOI: 10.3390/ijms19092796

Abstact

We have reported the propensity of a DNA sequence containing CCG repeats to form a stable i-motif tetraplex structure in the absence of ligands. Here we show that an i-motif DNA sequence may transition to a base-extruded duplex structure with a GGCC tetranucleotide tract when bound to the (CoII)-mediated dimer of chromomycin A3, CoII(Chro)₂. Biophysical experiments reveal that CCG trinucleotide repeats provide favorable binding sites for CoII(Chro)₂. In addition, water hydration and divalent metal ion (CoII) interactions also play a crucial role in the stabilization of CCG trinucleotide repeats (TNRs). Our data furnish useful structural information for the design of novel therapeutic strategies to treat neurological diseases caused by repeat expansions.

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Primary Citation of related structures