BMRB Entry 30012

Name: NMR structure of a new G-quadruplex forming sequence within the KRAS proto-oncogene promoter region
Published: 2016-03-14

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PDB ID: 5i2v
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30012
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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:

NMR structure of a new G-quadruplex forming sequence within the KRAS proto-oncogene promoter region

Deposition date:

2016-02-09

Original release date:

2016-03-14

Authors:

Salgado, G.; Kerkour, A.; Mergny, J.-L.

Citation:

Citation: Kerkour, Abdelaziz; Marquevielle, Julien; Ivashchenko, Stefaniia; Yatsunyk, Liliya; Mergny, Jean-Louis; Salgado, Gilmar. "High-resolution three-dimensional NMR structure of the KRAS proto-oncogene promoter reveals key features of a G-quadruplex involved in transcriptional regulation" J. Biol. Chem. 292, 8082-8091 (2017).
PubMed: 28330874

Assembly members:

Assembly members:
DNA (5'-D(*AP*GP*GP*GP*CP*GP*GP*TP*GP*TP*GP*GP*GP*AP*AP*TP*AP*GP*GP*GP*AP*A)-3'), polymer, 22 residues, 6986.514 Da.
POTASSIUM ION, non-polymer, 39.098 Da.

Natural source:

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: homo not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*AP*GP*GP*GP*CP*GP*GP*TP*GP*TP*GP*GP*GP*AP*AP*TP*AP*GP*GP*GP*AP*A)-3'): AGGGCGGTGTGGGAATAGGG AA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	218

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	potassium ion	2

Entities:

Entity 1, entity_1 22 residues - 6986.514 Da.

1

DA

DG

DC

DG

DT

DG

DT

2

DG

DA

DT

DA

DG

3

DA

Entity 2, potassium ion - 39.098 Da.

1

K

Samples:

sample_1: KRAS 22RT 2 mM; KRAS 22RT 15N, dG (5% 15N), 2 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 90 mM; pH: 6.6; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMBC	sample_1	isotropic	sample_conditions_1
1D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

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

ARIA, Linge, O'Donoghue and Nilges - structure calculation

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

CcpNMR, CCPN - data analysis

SPARKY, Goddard - chemical shift assignment

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

Bruker AvanceIII 700 MHz
Bruker AvanceIII 800 MHz