BMRB Entry 36640

Name: Solution NMR structure of the PTK7-binding DNA aptamer sgc8c
Published: 2025-12-12

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PDB ID: 8y0f
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36640
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR structure of the PTK7-binding DNA aptamer sgc8c

Deposition date:

2024-01-22

Original release date:

2025-12-12

Authors:

He, A.; Wan, L.; Guo, P.; Han, D.

Citation:

Citation: He, Axin; Wan, Liqi; Zhang, Yuchao; Yan, Zhenzhen; Guo, Pei; Han, Da; Tan, Weihong. "Structure-based investigation of a DNA aptamer targeting PTK7 reveals an intricate 3D fold guiding functional optimization." Proc. Natl. Acad. Sci. U. S. A. 121, e2404060121-e2404060121 (2024).
PubMed: 38985770

Assembly members:

Assembly members:
DNA, polymer, 41 residues, 12651.133 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis Host organism: unidentified

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA: ATCTAACTGCTGCGCCGCCG GGAAAATACTGTACGGTTAG A

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	106

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 41 residues - 12651.133 Da.

1

DA

DT

DC

DT

DA

DC

DT

DG

DC

2

DT

DG

DC

DG

DC

DG

DC

DG

3

DG

DA

DT

DA

DC

DT

4

DG

DT

DA

DC

DG

DT

DA

DG

5

DA

Samples:

sample_1: DNA 0.5 mM; Magnesium chloride 5 mM; sodium phosphate 10 mM; DSS 0.02 mM; D2O, [U-2H], 99.96%

sample_conditions_1: ionic strength: 15 mM; pH: 7; pressure: 1 bar; temperature: 277 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - chemical shift assignment

GROMACS, Abraham, Alekseenko, Bauer, Bergh, Blau, Briand, Doijade,... and Zhmurov - structure calculation

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

NMR spectrometers:

Bruker AVANCE 600 MHz