8R4W | pdb_00008r4w

(3+1) hybrid-2 G-quadruplex with a -(llp) loop progression

PDB DOI: https://doi.org/10.2210/pdb8R4W/pdb
BMRB: 34877
NAKB: 8R4W

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

Deposited: 2023-11-14 Released: 2023-12-27
Deposition Author(s): Jana, J., 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

Validation slider image for 8R4W

This is version 1.2 of the entry. See complete history.

Literature

Impact of loop length and duplex extensions on the design of hybrid-type G-quadruplexes.

Jana, J., Vianney, Y.M., Weisz, K.

(2024) Chem Commun (Camb) 60: 854-857

PubMed: 38131370 Search on PubMed
DOI: https://doi.org/10.1039/d3cc05625b
Primary Citation Related Structures:
8R4E, 8R4W

PubMed Abstract:
A G-rich core sequence G ₃-TCA-G ₃-T _1,2-G ₃-T _1,2-G ₃ can be designed to fold into a parallel or into two different (3+1) hybrid-type G-quadruplexes, among them an elusive topology with one lateral followed by two propeller loops. Favored folds can be rationalized based on the number of intervening thymidines and on additional complementary flanking sequences.

Organizational Affiliation

Institut für Biochemie, Universität Greifswald, Felix-Hausdorff Str. 4, Greifswald D-17489, Germany. weisz@uni-greifswald.de.

Macromolecule Content

Total Structure Weight: 7.91 kDa
Atom Count: 526
Modeled Residue Count: 25
Deposited Residue Count: 25
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (25-MER)	A	25	synthetic construct
Sequence Annotations Expand
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

Released Date: 2023-12-27

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	410497337

Revision History (Full details and data files)

Version 1.0: 2023-12-27
Type: Initial release
Version 1.1: 2024-01-10
Changes: Database references
Version 1.2: 2024-01-31
Changes: Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.