BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 34774

Title: An i-motif domain able to undergo pH-dependent conformational transitions (neutral structure)   PubMed: 36745195

Deposition date: 2022-12-01 Original release date: 2023-02-17

Authors: Serrano-Chacon, I.; Mir, B.; Colizzi, F.; Cupellini, L.; Orozco, M.; Escaja, N.; Gonzalez, C.

Citation: Serrano-Chacon, I.; Mir, B.; Colizzi, F.; Cupellini, L.; Orozco, M.; Escaja, N.; Gonzalez, C.. "pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs"  J. Am. Chem. Soc. 145, 3696-3705 (2023).

Assembly members:
entity_1, polymer, 22 residues, 6629.263 Da.

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

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: CXGTTCXGTTTTTCCGTTCC GT

Data sets:
Data typeCount
1H chemical shifts172

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 22 residues - 6629.263 Da.

1   DCDNRDGDTDTDCDNRDGDTDT
2   DTDTDTDCDCDGDTDTDCDC
3   DGDT

Samples:

sample_1: DNA (5'-D(*CP*(DNR)P*GP*TP*TP*CP*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*CP*CP*GP*T)-3') 500 uM; sodium phosphate 10 mM; DSS 0.5 v/v

sample_2: DNA (5'-D(*CP*(DNR)P*GP*TP*TP*CP*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*CP*CP*GP*T)-3') 500 uM; sodium phosphate 10 mM; DSS 0.5 v/v

sample_conditions_1: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 10 mM; pH: 7; pressure: 1 atm; temperature: 278 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_1isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_2
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_2
2D 1H-1H NOESYsample_2isotropicsample_conditions_2
2D 1H-1H COSYsample_2isotropicsample_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 600 MHz