BMRB Entry 34616

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34616
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Title:
The structure of an i-motif/duplex junction at neutral pH
Deposition date:
2021-04-08
Original release date:
2021-09-01
Authors:
Serrano-Chacon, I.; Mir, B.; Escaja, N.; Gonzalez, C.
Citation:

Citation: Serrano-Chacon, I.; Mir, B.; Escaja, N.; Gonzalez, C.. "Structure of i-Motif/Duplex Junctions at Neutral pH"  J. Am. Chem. Soc. 143, 12919-12923 (2021).
PubMed: 34370473

Assembly members:

Assembly members:
entity_1, polymer, 35 residues, 10583.800 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: CXXGTTTXXTCGCGAAGCAT TCGCGXCCGTTTCCT

Data sets:
Data typeCount
1H chemical shifts222

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 35 residues - 10583.800 Da.

1   DCDNRDNRDGDTDTDTDNRDNRDT
2   DCDGDCDGDADADGDCDADT
3   DTDCDGDCDGDNRDCDCDGDT
4   DTDTDCDCDT

Samples:

sample_1: I-motif/duplex junction (IDJ) 0.5 mM; sodium phosphate 10 mM; DSS 0.5 % v/v

sample_conditions_1: ionic strength: 10 mM; pH: 7.0; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 10 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H COSYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D 1H-1H TOCSYsample_1isotropicsample_conditions_2
2D 1H-1H COSYsample_1isotropicsample_conditions_2

Software:

TopSpin, Bruker Biospin - collection, processing

Sparky, Goddard - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

3DNA, Lu and Olson - data analysis

MOLMOL, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

  • Bruker AVANCE III 600 MHz