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- PDB-6t2g: NMR structure of KRAS32R G25T conformer G-quadruplex within KRAS ... -

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Basic information

Entry
Database: PDB / ID: 6t2g
TitleNMR structure of KRAS32R G25T conformer G-quadruplex within KRAS promoter region
ComponentsKRAS32R G25T
KeywordsDNA / KRAS G-quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsMarquevielle, J. / Salgado, G.
Funding support France, 1items
OrganizationGrant numberCountry
French League Against Cancer France
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structure of two G-quadruplexes in equilibrium in the KRAS promoter.
Authors: Marquevielle, J. / Robert, C. / Lagrabette, O. / Wahid, M. / Bourdoncle, A. / Xodo, L.E. / Mergny, J.L. / Salgado, G.F.
History
DepositionOct 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KRAS32R G25T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3253
Polymers10,2471
Non-polymers782
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area260 Å2
ΔGint-0 kcal/mol
Surface area6080 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 750structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain KRAS32R G25T


Mass: 10246.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic22D 1H-1H NOESY
122anisotropic22D 1H-15N HSQC
132anisotropic22D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12 mM KRAS32R G25T no labelled, 90% H2O/10% D2OKRAS32R G25T90% H2O/10% D2O
solution20.5 mM [U-99% 13C; U-99% 15N] KRAS32R G25T, 90% H2O/10% D2OKRAS32R G25T 15N 13C90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMKRAS32R G25T no labellednatural abundance1
0.5 mMKRAS32R G25T[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 50 KCl ; 10 KPi mM / Label: KRAS32R G25T / pH: 6.66 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
Amber12Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
SparkyGoddardchemical shift assignment
TopSpinBruker Biospinprocessing
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 750 / Conformers submitted total number: 10

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