BMRB Entry 34798

Name: Structure of an i-motif domain with the cytosine analog 1,3-diaza-2-oxophenoxacione (tC) at neutral pH
Published: 2024-02-02

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PDB ID: 8ofc
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34798
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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:

Structure of an i-motif domain with the cytosine analog 1,3-diaza-2-oxophenoxacione (tC) at neutral pH

Deposition date:

2023-03-15

Original release date:

2024-02-02

Authors:

Mir, B.; Serrano-Chacon, I.; Terrazas, M.; Gandioso, A.; Garavis, M.; Orozco, M.; Escaja, N.; Gonzalez, C.

Citation:

Citation: Mir, Bartomeu; Serrano-Chacon, Israel; Medina, Pedro; Macaluso, Veronica; Terrazas, Montserrat; Gandioso, Albert; Garavis, Miguel; Orozco, Modesto; Escaja, Nuria; Gonzalez, Carlos. "Site-specific incorporation of a fluorescent nucleobase analog enhances i-motif stability and allows monitoring of i-motif folding inside cells" Nucleic Acids Res. 52, 3375-3389 (2024).
PubMed: 38366792

Assembly members:

Assembly members:
entity_1, polymer, 22 residues, 6719.344 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: CXGTTCXGTTTTTCCGTTCX GT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	177

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 - 6719.344 Da.

1

DC

YCO

DG

DT

DC

DNR

DG

DT

2

DT

DC

DG

DT

DC

DNR

3

DG

DT

Samples:

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

sample_2: DNA (5'-D(*CP*(YCO)P*GP*TP*TP*CP*(DNR)P*GP*TP*TP*TP*TP*TP*CP*CP*GP*TP*TP*CP*(DNR)P*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: 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_1
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_1

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

MOLMOL, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

Bruker AVANCE 600 MHz