BMRB Entry 34843

Name: RNA G-quadruplex from the 5&#039;-UTR of human tyrosine kinase 2 (TYK2)
Published: 2024-02-28

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PDB ID: 8q4o
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34843
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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:

RNA G-quadruplex from the 5'-UTR of human tyrosine kinase 2 (TYK2)

Deposition date:

2023-08-07

Original release date:

2024-02-28

Authors:

Toplishek, M.; Kocman, V.

Citation:

Citation: Orehova, Maria; Plavec, Janez; Kocman, VojC. "High-Resolution Structure of RNA G-Quadruplex Containing Unique Structural Motifs Originating from the 5'-UTR of Human Tyrosine Kinase 2 (TYK2)" ACS Omega 9, 7215-7229 (2024).
PubMed: 38371751

Assembly members:

Assembly members:
entity_1, polymer, 23 residues, 7507.481 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: CGGUAGCGGGUAUGGGUCCG GGU

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	113

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 23 residues - 7507.481 Da.

1

C

G

U

A

G

C

G

2

U

A

U

G

U

C

G

3

G

U

Samples:

sample_1: RNA (5'-R(*CP*GP*GP*UP*AP*GP*CP*GP*GP*GP*UP*AP*UP*GP*GP*GP*UP*CP*CP*GP*GP*GP*U)-3') 0.5 ± 0.05 mM; potassium phosphate 10 ± 1 mM; potassium chloride 10 ± 1 mM

sample_2: RNA (5'-R(*CP*GP*GP*UP*AP*GP*CP*GP*GP*GP*UP*AP*UP*GP*GP*GP*UP*CP*CP*GP*GP*GP*U)-3') 1.0 ± 0.1 mM; potassium phosphate 10 ± 1 mM; potassium chloride 10 ± 1 mM

sample_3: RNA (5'-R(*CP*GP*GP*UP*AP*GP*CP*GP*GP*GP*UP*AP*UP*GP*GP*GP*UP*CP*CP*GP*GP*GP*U)-3') 0.8 ± 0.08 mM; potassium phosphate 10 ± 1 mM; potassium chloride 10 ± 1 mM; Pf1 phage 17 ± 1 mg/mL

sample_conditions_1: ionic strength: 20 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_2	isotropic	sample_conditions_1
IPAP-edited HSQC	sample_3	anisotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

NMRFAM-SPARKY, National Magnetic Resonance Facility at Madison - chemical shift assignment

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

NMR spectrometers:

Bruker AVANCE NEO 600 MHz