5XEW

Crystal structure of the [Ni2+-(chromomycin A3)2]-CCG repeats complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.751 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation

Tseng, W.H.Chang, C.K.Wu, P.C.Hu, N.J.Lee, G.H.Tzeng, C.C.Neidle, S.Hou, M.H.

(2017) Angew. Chem. Int. Ed. Engl. 56: 8761-8765

  • DOI: 10.1002/anie.201703989

  • PubMed Abstract: 
  • Small-molecule compounds targeting trinucleotide repeats in DNA have considerable potential as therapeutic or diagnostic agents against many neurological diseases. NiII (Chro)2 (Chro=chromomycin A3) binds specifically to the minor groove of (CCG)n re ...

    Small-molecule compounds targeting trinucleotide repeats in DNA have considerable potential as therapeutic or diagnostic agents against many neurological diseases. NiII (Chro)2 (Chro=chromomycin A3) binds specifically to the minor groove of (CCG)n repeats in duplex DNA, with unique fluorescence features that may serve as a probe for disease detection. Crystallographic studies revealed that the specificity originates from the large-scale spatial rearrangement of the DNA structure, including extrusion of consecutive bases and backbone distortions, with a sharp bending of the duplex accompanied by conformational changes in the NiII chelate itself. The DNA deformation of CCG repeats upon binding forms a GGCC tetranucleotide tract, which is recognized by NiII (Chro)2 . The extruded cytosine and last guanine nucleotides form water-mediated hydrogen bonds, which aid in ligand recognition. The recognition can be accounted for by the classic induced-fit paradigm.


    Organizational Affiliation

    Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*AP*A)-3')A,B13synthetic construct
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1GL
Query on 1GL

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A, B
4-O-METHYL-2,6-DIDEOXY-ALPHA-D-GALACTO-HEXOPYRANOSE
C7 H14 O4
CDRBUGSWTNDUSM-JWXFUTCRSA-N
 Ligand Interaction
ERI
Query on ERI

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A, B
4-O-ACETYL-2,6-DIDEOXY-3-C-METHYL-BETA-L-ARABINO-HEXOPYRANOSE
C9 H16 O5
YJOQPCPEUGDGFS-VHKYIWFCSA-N
 Ligand Interaction
ARI
Query on ARI

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Download CCD File 
A, B
[O4]-ACETOXY-2,3-DIDEOXYFUCOSE
C8 H14 O4
NNWBJOVUTCFRGH-LPBLVHEISA-N
 Ligand Interaction
CPH
Query on CPH

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A, B
(1S)-5-deoxy-1-O-methyl-1-C-[(2R,3S)-3,5,7,10-tetrahydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-D-xylulose
None
C21 H24 O9
AOCJXLJIUYHXRS-PKRZCTMMSA-N
 Ligand Interaction
CDR
Query on CDR

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Download CCD File 
A, B
2,3-DIDEOXYFUCOSE
C6 H12 O3
ZCYMCBOUZXAAJG-NGJCXOISSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.751 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.207 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 48.291α = 90.00
b = 48.291β = 90.00
c = 83.356γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data processing
HKL-2000data scaling
Blu-Icedata collection
PHENIXrefinement
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Database references
  • Version 1.2: 2017-07-19
    Type: Database references