BMRB Entry 35011

Name: A tetrameric i-motif structure formed by dTdCdCfrCdCdC
Published: 2025-10-08

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PDB ID: 9s6z
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR35011
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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:

A tetrameric i-motif structure formed by dTdCdCfrCdCdC

Deposition date:

2025-08-01

Original release date:

2025-10-08

Authors:

Ugedo, C.; Dominguez, A.; Gomez-Pinto, I.; Eritja, R.; Avino, A.; Gonzalez, C.

Citation:

Citation: Ugedo, C.; Dominguez, A.; Gomez-Pinto, I.; Eritja, R.; Gonzalez, C.; Avino, A.. "The Effect of 2'F-RNA on I-Motif Structure and Stability." Molecules 30, .-. (2025).
PubMed: 40942089

Assembly members:

Assembly members:
entity_1, polymer, 6 residues, 1724.143 Da.
entity_2, polymer, 6 residues, 1726.159 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: TCCXXC
entity_2: TXXXCX

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
19F chemical shifts	1
1H chemical shifts	58

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
3	unit_3	2
4	unit_4	2

Entities:

Entity 1, unit_1 6 residues - 1724.143 Da.

1

DT

DC

CFZ

DNR

DC

Entity 2, unit_3 6 residues - 1726.159 Da.

1

DT

DNR

CFZ

DC

DNR

Samples:

sample_1: sodium phosphate 10 mM; potassium chloride 50 mM; iFRNA1 nucleotide 0.5 mM; iFRNA1 nucleotide 0.5 mM

sample_conditions_1: ionic strength: 60 mM; pH: 5; pressure: 1 atm; temperature: 178 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D NOESY	sample_1	anisotropic	sample_conditions_1
2D HOESY	sample_1	anisotropic	sample_conditions_1
2D TOCSY	sample_1	anisotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - refinement

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

NMRFAM-SPARKY, National Magnetic Resonance Facility, University of Wisconsin Madison - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE NEO 600 MHz
Bruker AVANCE NEO 800 MHz