BMRB Entry 34735

Name: Dimeric i-motif from 2'Farabinocytidine-modified TC5
Published: 2023-02-21

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PDB ID: 7zyx
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34735
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:

Dimeric i-motif from 2'Farabinocytidine-modified TC5

Deposition date:

2022-05-25

Original release date:

2023-02-21

Authors:

Garavis, M.; El Khoury, R.; Damha, M.; Gonzalez, C.

Citation:

Citation: El-Khoury, Roberto; Macaluso, Veronica; Hennecker, Christopher; Mittermaier, Anthony; Orozco, Modesto; Gonzalez, Carlos; Garavis, Miguel; Damha, Masad. "i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F...H and O...H hydrogen bonds" Commun. Chem. 6, 31-31 (2023).
PubMed: 36797370

Assembly members:

Assembly members:
entity_1, polymer, 6 residues, 1795.099 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: TXXXXX

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
19F chemical shifts	10
1H chemical shifts	116

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	1

Entities:

Entity 1, unit_1 6 residues - 1795.099 Da.

1

DT

CFL

Samples:

sample_1: NaPi 10 mM

sample_conditions_1: ionic strength: 10 mM; pH: 5.0; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-19F HOESY	sample_1	isotropic	sample_conditions_1

Software:

NMRFAM-SPARKY, Lee W, Tonelli M, Markley JL. - chemical shift assignment, peak picking

TopSpin, Bruker Biospin - collection

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

NMR spectrometers:

Bruker AVANCE NEO 600 MHz
Bruker AVANCE III HD 600 MHz