BMRB Entry 34863

Name: Solution structure of a bimolecular quadruplex-duplex hybrid containing a V-shaped loop
Published: 2024-01-31

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PDB ID: 8qkx
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34863
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of a bimolecular quadruplex-duplex hybrid containing a V-shaped loop

Deposition date:

2023-09-18

Original release date:

2024-01-31

Authors:

Vianney, Y.; Weisz, K.

Citation:

Citation: Agustin, D.; Vianney, Y.; Weisz, K.; Wahjudi, M.. "Structural Aspects of Split G-Quadruplexes in Quadruplex-Duplex Hybrid Systems" .

Assembly members:

Assembly members:
entity_1, polymer, 24 residues, 7498.800 Da.
entity_2, polymer, 14 residues, 4366.836 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: CTCCAGCTGGGTGAGGGGCT GGGT
entity_2: TTGGAGCTGGAGTT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	42
1H chemical shifts	261

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 24 residues - 7498.800 Da.

1

DC

DT

DC

DA

DG

DC

DT

DG

2

DG

DT

DG

DA

DG

DC

DT

3

DG

DT

Entity 2, unit_2 14 residues - 4366.836 Da.

1

DT

DG

DA

DG

DC

DT

DG

2

DA

DG

DT

Samples:

sample_1: DNA (5'-D(CTCCAGCTGGGTGAGGGGCTGGGT)-3') 0.42 mM; DNA (5'-D(TTGGAGCTGGAGTT)-3') 0.42 mM

sample_2: DNA (5'-D(CTCCAGCTGGGTGAGGGGCTGGGT)-3'), [U-13C; U-15N]-Gua, 0.22 mM; DNA (5'-D(TTGGAGCTGGAGTT)-3') 0.22 mM

sample_3: DNA (5'-D(CTCCAGCTGGGTGAGGGGCTGGGT)-3') 0.22 mM; DNA (5'-D(TTGGAGCTGGAGTT)-3'), [U-13C; U-15N]-Gua, 0.22 mM

sample_4: DNA (5'-D(CTCCAGCTGGGTGAGGGGCTGGGT)-3') 0.22 mM; DNA (5'-D(TTGGAGCTGGAGTT)-3'), [U-13C; U-15N]-Gua, 0.22 mM

sample_conditions_1: ionic strength: 120 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1

Software:

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment

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