6CCW

Hybrid-2 form Human Telomeric G Quadruplex in Complex with Epiberberine

  • Classification: DNA
  • Organism(s): Homo sapiens

  • Deposited: 2018-02-07 Released: 2018-06-20 
  • Deposition Author(s): Lin, C., Yang, D.Z.
  • Funding Organization(s): National Institutes of Health/National Human Genome Research Institute 

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular Recognition of the Hybrid-2 Human Telomeric G-Quadruplex by Epiberberine: Insights into Conversion of Telomeric G-Quadruplex Structures.

Lin, C.Wu, G.Wang, K.Onel, B.Sakai, S.Shao, Y.Yang, D.

(2018) Angew. Chem. Int. Ed. Engl. 57: 10888-10893

  • DOI: 10.1002/anie.201804667

  • PubMed Abstract: 
  • Human telomeres can form DNA G-quadruplex (G4), an attractive target for anticancer drugs. Human telomeric G4s bear inherent structure polymorphism, challenging for understanding specific recognition by ligands or proteins. Protoberberines are medici ...

    Human telomeres can form DNA G-quadruplex (G4), an attractive target for anticancer drugs. Human telomeric G4s bear inherent structure polymorphism, challenging for understanding specific recognition by ligands or proteins. Protoberberines are medicinal natural-products known to stabilize telomeric G4s and inhibit telomerase. Here we report epiberberine (EPI) specifically recognizes the hybrid-2 telomeric G4 predominant in physiologically relevant K+ solution and converts other telomeric G4 forms to hybrid-2, the first such example. Our NMR structure in K+ solution shows EPI binding induces extensive rearrangement of the previously disordered 5' flanking and loop segments to form an unprecedented four-layer binding pocket specific to the hybrid-2 telomeric G4; EPI recruits the -1 adenine to form a "quasi-triad" intercalated between the external tetrad and a T:T:A triad, capped by a T:T base-pair. Our study provides structural basis for small-molecule drug design targeting the human telomeric G4.


    Organizational Affiliation

    UNITED STATES.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (26-MER)A26Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EWV
Query on EWV

Download SDF File 
Download CCD File 
A
Epiberberine
8,9-dimethoxy-11,12-dihydro-2H-[1,3]dioxolo[4,5-h]isoquinolino[2,1-b]isoquinolin-13-ium
C20 H18 N O4
FPJQGFLUORYYPE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-02-07 
  • Released Date: 2018-06-20 
  • Deposition Author(s): Lin, C., Yang, D.Z.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited States--

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references