6R9K

A quadruplex hybrid structure with lpp loop orientation and 3 syn residues

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

  • Deposited: 2019-04-03 Released: 2019-07-03 
  • Deposition Author(s): Karg, B., Weisz, K.
  • Funding Organization(s): German Research Foundation

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Duplex-Guided Refolding into Novel G-Quadruplex (3+1) Hybrid Conformations.

Karg, B., Mohr, S., Weisz, K.

(2019) Angew Chem Int Ed Engl 58: 11068-11071

  • DOI: https://doi.org/10.1002/anie.201905372
  • Primary Citation of Related Structures:  
    6R9K, 6R9L

  • PubMed Abstract: 

    The oligomer d(GCGTG 3 TCAG 3 TG 3 TG 3 ACGC) with short complementary flanking sequences at the 5'- and 3'-ends was shown to fold into three different DNA G-quadruplex species. In contrast, a corresponding oligomer that lacks base complementarity between the two overhang sequences folds into a single parallel G-quadruplex. The three coexisting quadruplex structures were unambiguously identified and structurally characterized through detailed spectral comparisons with well-defined G-quadruplexes formed upon the deliberate incorporation of syn-favoring 8-bromoguanosine analogues into specific positions of the G-core. Two (3+1) hybrid structures coexist with the parallel fold and feature a novel lateral-propeller-propeller loop architecture that has not yet been confirmed experimentally. Both hybrid quadruplexes adopt the same topology and only differ in their pattern of anti→syn transitions and tetrad stackings.

    • Organizational Affiliation: 

    Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (25-MER)25Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • 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 FoundationGermanydfg we 1933/15-1

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.3: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.4: 2021-06-23
    Changes: Data collection
  • Version 1.5: 2024-05-15
    Changes: Data collection, Database references