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- PDB-7alu: NMR structure of a DNA G-quadruplex containing two SP1 binding si... -

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Basic information

Entry
Database: PDB / ID: 7alu
TitleNMR structure of a DNA G-quadruplex containing two SP1 binding sites from HIV-1 promoter
ComponentsDNA (5'-D(*AP*GP*GP*GP*AP*GP*GP*TP*GP*TP*GP*GP*CP*CP*TP*GP*GP*GP*CP*GP*GP*G)-3')
KeywordsDNA / Virus / HIV-1 / G-quadruplex / SP1
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / molecular dynamics
AuthorsDe Rache, A. / Marquevielle, J. / Amrane, S.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANRS / AAP 2019-2 / ECTZ103899 France
CitationJournal: J.Mol.Biol. / Year: 2023
Title: Structure of a DNA G-quadruplex that modulates SP1 binding sites architecture in HIV-1 promoter.
Authors: De Rache, A. / Marquevielle, J. / Bouaziz, S. / Vialet, B. / Andreola, M.L. / Mergny, J.L. / Amrane, S.
History
DepositionOct 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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*AP*GP*GP*TP*GP*TP*GP*GP*CP*CP*TP*GP*GP*GP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0493
Polymers6,9701
Non-polymers782
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
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 DNA (5'-D(*AP*GP*GP*GP*AP*GP*GP*TP*GP*TP*GP*GP*CP*CP*TP*GP*GP*GP*CP*GP*GP*G)-3')


Mass: 6970.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#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
112anisotropic32D 1H-1H NOESY
121anisotropic32D 1H-1H NOESY
131anisotropic22D 1H-13C HSQC aromatic
141anisotropic22D 1H-13C HSQC aliphatic
151anisotropic22D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12.4 mM None HIVpro3, 100% D2OHIVpro3_D2O100% D2O
solution2857 uM None HIVpro3, 90% H2O/10% D2OHIVpro3_H2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.4 mMHIVpro3None1
857 uMHIVpro3None2
Sample conditionsIonic strength: 70 KCl; 20 KPi mM / Label: HIVpro3 / pH: 6.9 Not defined / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III4001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCE IIIBrukerAVANCE III8003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospindata analysis
SparkyGoddardchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 4
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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