BMRB Entry 34772

Name: An i-motif domain able to undergo pH-dependent conformational transitions (acidic structure)
Published: 2023-02-14

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PDB ID: 8bqy
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34772
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

An i-motif domain able to undergo pH-dependent conformational transitions (acidic structure)

Deposition date:

2022-11-22

Original release date:

2023-02-14

Authors:

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

Citation:

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).
PubMed: 36745195

Assembly members:

Assembly members:
entity_1, polymer, 22 residues, 6631.280 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: CXGTTXXGTTTTTCCGTTXC GT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	183

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 22 residues - 6631.280 Da.

1

DC

DNR

DG

DT

DNR

DG

DT

2

DT

DC

DG

DT

DNR

DC

3

DG

DT

Samples:

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

sample_conditions_1: ionic strength: 10 mM; pH: 5; pressure: 1 atm; temperature: 278 K

sample_conditions_2: ionic strength: 10 mM; pH: 5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_2
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
2D DQF-COSY	sample_2	isotropic	sample_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