BMRB Entry 34900

Name: Structure of a quadruplex-duplex hybrid with a (-pd+l) loop progression
Published: 2024-03-21

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PDB ID: 8s1w
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34900
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of a quadruplex-duplex hybrid with a (-pd+l) loop progression

Deposition date:

2024-02-16

Original release date:

2024-03-21

Authors:

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

Citation:

Citation: Vianney, Y.; Jana, J.; Weisz, K.. "A pH-Responsive Topological Switch Based on a DNA Quadruplex-Duplex Hybrid" Chemistry 30, e202400722-e202400722 (2024).
PubMed: 38497675

Assembly members:

Assembly members:
entity_1, polymer, 33 residues, 10467.536 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GGGCGCGAAGCATTCGCGGG GTTAGXGTTAGGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	46
1H chemical shifts	205

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 33 residues - 10467.536 Da.

1

DG

DC

DG

DC

DG

DA

DG

2

DC

DA

DT

DC

DG

DC

DG

3

DG

DT

DA

DG

BGM

DG

DT

DA

4

DG

Samples:

sample_1: DNA (33-MER) 0.3 mM; DNA (33-MER), [U-10% 13C; U-10% 15N] deoxyguanosine, 0.2 mM; potassium phosphate buffer 20 mM; KCl 100 mM

sample_conditions_1: ionic strength: 120 mM; pH: 7.9; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
1H-15N HMQC	sample_1	isotropic	sample_conditions_1

Software:

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment, peak picking

Amber v18, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement, structure calculation

TopSpin v4.0.7, Bruker Biospin - processing

NMR spectrometers:

Bruker AVANCE NEO 600 MHz