BMRB Entry 36374

Name: Quadruplex-duplex hybrid structure in the PIM1 gene, Form 1
Published: 2025-10-24

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PDB ID: 7cv3
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36374
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Quadruplex-duplex hybrid structure in the PIM1 gene, Form 1

Deposition date:

2020-08-25

Original release date:

2025-10-24

Authors:

Winnerdy, F.; Tan, D.; Lim, K.; Phan, A.

Citation:

Citation: Tan, Derrick; Winnerdy, Fernaldo; Lim, Kah Wai; Phan, Anh Tuan. "Coexistence of two quadruplex-duplex hybrids in the PIM1 gene." Nucleic Acids Res. 48, 11162-11171 (2020).
PubMed: 32976598

Assembly members:

Assembly members:
PIM1 promoter, Form 1, polymer, 27 residues, 8506.419 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PIM1 promoter, Form 1: GCGGGAGGGCGCGCCAGCGG GGTCGGG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	209

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 27 residues - 8506.419 Da.

1

DG

DC

DG

DA

DG

DC

2

DG

DC

DG

DC

DA

DG

DC

DG

3

DG

DT

DC

DG

Samples:

sample_H2O: GC-PIM1 2 mM; KCl 70 mM; potassium phosphate 20 mM; DSS 50 uM; H2O 90%; D2O, [U-2H], 10%

sample_D2O: GC-PIM1 2 mM; KCl 70 mM; potassium phosphate 20 mM; DSS 50 uM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 100 mM; pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_H2O	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_D2O	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_D2O	isotropic	sample_conditions_1

Software:

TopSpin v2.1, Bruker Biospin - collection

TopSpin v4.0, Bruker Biospin - processing

NMRFAM-SPARKY, Lee, Tonelli, Markley - peak picking

NMRFAM-SPARKY, Lee, Tonelli, Markley - chemical shift assignment

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker AVANCE II 600 MHz