3R6R

Structure of the complex of an intramolecular human telomeric DNA with Berberine formed in K+ solution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of human telomeric DNA complexed with berberine: an interesting case of stacked ligand to G-tetrad ratio higher than 1:1.

Bazzicalupi, C.Ferraroni, M.Bilia, A.R.Scheggi, F.Gratteri, P.

(2013) Nucleic Acids Res. 41: 632-638

  • DOI: 10.1093/nar/gks1001

  • PubMed Abstract: 
  • The first crystal structure of human telomeric DNA in complex with the natural alkaloid berberine, produced by different plant families and used in folk medicine for millennia, was solved by X-ray diffraction method. The G-quadruplex unit features al ...

    The first crystal structure of human telomeric DNA in complex with the natural alkaloid berberine, produced by different plant families and used in folk medicine for millennia, was solved by X-ray diffraction method. The G-quadruplex unit features all-parallel strands. The overall folding assumed by DNA is the same found in previously reported crystal structures. Similarly to previously reported structures the ligand molecules were found to be stacked onto the external 5' and 3'-end G-tetrads. However, the present crystal structure highlighted for the first time, the presence of two berberine molecules in the two binding sites, directly interacting with each tetrad. As a consequence, our structural data point out a 2:1 ligand to G-tetrad molar ratio, which has never been reported before in a telomeric intramolecular quadruplex structure.


    Organizational Affiliation

    Department of Chemistry Ugo Schiff, University of Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Firenze, Italy.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (22-mer)A22N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
BER
Query on BER

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Download CCD File 
A
BERBERINE
C20 H18 N O4
YBHILYKTIRIUTE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.215 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 65.620α = 90.00
b = 65.620β = 90.00
c = 41.810γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOLREPphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2013-01-30
    Type: Database references