7KLP

Crystal structure of a three-tetrad, parallel, K+ stabilized human telomeric G-quadruplex

  • Classification: DNA
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2020-10-30 Released: 2020-12-30 
  • Deposition Author(s): Yatsunyk, L.A., Li, K.S., Chen, E.V.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Water spines and networks in G-quadruplex structures.

Li, K.Yatsunyk, L.Neidle, S.

(2021) Nucleic Acids Res 49: 519-528

  • DOI: 10.1093/nar/gkaa1177
  • Primary Citation of Related Structures:  
    7KLP, 6XT7

  • PubMed Abstract: 
  • Quadruplex DNAs can fold into a variety of distinct topologies, depending in part on loop types and orientations of individual strands, as shown by high-resolution crystal and NMR structures. Crystal structures also show associated water molecules. W ...

    Quadruplex DNAs can fold into a variety of distinct topologies, depending in part on loop types and orientations of individual strands, as shown by high-resolution crystal and NMR structures. Crystal structures also show associated water molecules. We report here on an analysis of the hydration arrangements around selected folded quadruplex DNAs, which has revealed several prominent features that re-occur in related structures. Many of the primary-sphere water molecules are found in the grooves and loop regions of these structures. At least one groove in anti-parallel and hybrid quadruplex structures is long and narrow and contains an extensive spine of linked primary-sphere water molecules. This spine is analogous to but fundamentally distinct from the well-characterized spine observed in the minor groove of A/T-rich duplex DNA, in that every water molecule in the continuous quadruplex spines makes a direct hydrogen bond contact with groove atoms, principally phosphate oxygen atoms lining groove walls and guanine base nitrogen atoms on the groove floor. By contrast, parallel quadruplexes do not have extended grooves, but primary-sphere water molecules still cluster in them and are especially associated with the loops, helping to stabilize loop conformations.


    Organizational Affiliation

    UCL School of Pharmacy, University College London, London WC1N 1AX, UK.



Macromolecules
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
telomeric DNAA22Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.145 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.686α = 90
b = 56.686β = 90
c = 42.31γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata reduction
XDSdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States1R15CA208676-01A1

Revision History 

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references