7ATZ | pdb_00007atz

G-quadruplex with V-shaped loop from the first repeat of KCNN4 minisatellite

  • Classification: DNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2020-11-02 Released: 2021-04-21 
  • Deposition Author(s): Vianney, Y.M., Weisz, K.
  • Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

First Tandem Repeat of a Potassium Channel KCNN4 Minisatellite Folds into a V-Loop G-Quadruplex Structure.

Vianney, Y.M., Weisz, K.

(2021) Biochemistry 60: 1337-1346

  • DOI: https://doi.org/10.1021/acs.biochem.1c00043
  • Primary Citation Related Structures: 
    7ATZ

  • PubMed Abstract: 

    The KCNN4 gene encoding a potassium channel protein whose expression has been correlated with tumor progression was found to comprise a guanine-rich minisatellite region with the ability to form a putative G-quadruplex (G4). Given the suggested regulatory role of G4s in gene expression, G-quadruplex formation for the polymorphic first repeat of the minisatellite was studied by nuclear magnetic resonance spectroscopy. A stable G-quadruplex of a truncated mutant sequence was shown to represent one of several coexisting species of the wild-type sequence. The high-resolution structure features a noncanonical G4 with a broken G-column and a V-shaped loop. The presence of a 3'-flanking thymidine interacting with the lateral loop preceding the V loop seems to be critical for the formation of this G4 topology. On the contrary, an additional 5'-flanking residue disfavored but still allowed folding into the V-loop structure. The latter may therefore serve as a putative therapeutic target in strategies for G4-based modulation of KCNN4 expression.

    • Organizational Affiliation: 
    • Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany.

Macromolecule Content 

  • Total Structure Weight: 7.3 kDa 
  • Atom Count: 486 
  • Modeled Residue Count: 23 
  • Deposited Residue Count: 23 
  • Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*GP*TP*CP*TP*GP*AP*GP*GP*GP*AP*GP*AP*GP*GP*GP*GP*CP*TP*GP*GP*GP*T)-3')23synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyINST 292/138-1

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Database references
  • Version 1.2: 2021-05-12
    Changes: Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references