5YZE

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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This is version 3.1 of the entry. See complete history. 


Literature

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.

(2018) Int J Mol Sci 19

  • DOI: https://doi.org/10.3390/ijms19092796
  • Primary Citation of Related Structures:  
    5YZE

  • PubMed Abstract: 

    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 (Co II )-mediated dimer of chromomycin A3, Co II (Chro)₂. Biophysical experiments reveal that CCG trinucleotide repeats provide favorable binding sites for Co II (Chro)₂. In addition, water hydration and divalent metal ion (Co II ) 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.

    • Organizational Affiliation: 

    Institute of Biotechnology, National Chung-Hsing University, Taichung 402, Taiwan. dodochinchin@gmail.com.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')
A, B
11synthetic construct
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol
C, F
3N/A
Glycosylation Resources
GlyTouCan:  G76712GN
GlyCosmos:  G76712GN
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate
D, E
2N/A
Glycosylation Resources
GlyTouCan:  G66610ZG
GlyCosmos:  G66610ZG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.401α = 90
b = 46.401β = 90
c = 73.822γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SHELXDEphasing
HKL-2000data scaling
Cootmodel building
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2021-01-20
    Changes: Derived calculations, Polymer sequence, Structure summary
  • Version 3.1: 2024-03-27
    Changes: Data collection, Database references