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- PDB-5i2v: NMR structure of a new G-quadruplex forming sequence within the K... -

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Basic information

Entry
Database: PDB / ID: 5i2v
TitleNMR structure of a new G-quadruplex forming sequence within the KRAS proto-oncogene promoter region
ComponentsDNA (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')
KeywordsDNA / G-quadruplex / KRAS / proto-oncogene / cancer target
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSalgado, G.F. / Kerkour, A. / Mergny, J.-L.
Funding support France, 3items
OrganizationGrant numberCountry
Inserm - University of BordeauxChair Mixte Inserm-U. Bordeaux France
Conseil regional de Aquitaine France
French National Research Agency France
CitationJournal: J. Biol. Chem. / Year: 2017
Title: High-resolution three-dimensional NMR structure of the KRAS proto-oncogene promoter reveals key features of a G-quadruplex involved in transcriptional regulation.
Authors: Kerkour, A. / Marquevielle, J. / Ivashchenko, S. / Yatsunyk, L.A. / Mergny, J.L. / Salgado, G.F.
History
DepositionFeb 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3May 24, 2017Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5May 8, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.6Sep 30, 2020Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.7Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0653
Polymers6,9871
Non-polymers782
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area270 Å2
ΔGint-0 kcal/mol
Surface area4770 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 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')


Mass: 6986.514 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA G-quadruplex from the nuclease hypersensitive element of KRAS promotor region
Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-1H NOESY
181isotropic12D 1H-1H NOESY
121isotropic22D 1H-1H COSY
131isotropic22D 1H-13C HSQC
141isotropic22D 1H-1H TOCSY
151isotropic22D 1H-15N HSQC
161isotropic12D 1H-13C HMBC
171isotropic11D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 2 mM KRAS 22RT, 2 mM dG (5% 15N) KRAS 22RT 15N, 90% H2O/10% D2O
Label: no / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMKRAS 22RTnatural abundance1
2 mMKRAS 22RT 15NdG (5% 15N)1
Sample conditionsDetails: 20 mM potassium phosphate pH ~6.6 with 70 mM KCl / Ionic strength: 90 mM / Ionic strength err: 2 / Label: Phosphate buffer / pH: 6.6 / PH err: 0.1 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNdata analysis
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 11

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