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- PDB-7ps8: NMR Structure of the U3 RNA G-quadruplex -

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Basic information

Entry
Database: PDB / ID: 7ps8
TitleNMR Structure of the U3 RNA G-quadruplex
ComponentsRNA (5'-R(*CP*AP*GP*GP*GP*AP*GP*GP*UP*GP*UP*GP*GP*CP*CP*UP*GP*GP*GP*CP*GP*GP*G)-3')
KeywordsVIRUS / HIV-1
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesHIV-1 06TG.HT008 (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsMarquevielle, J. / Amrane, S.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de Recherches Sur le Sida et les Hepatites Virales (ANRS)ECTZ103899 France
CitationJournal: To Be Published
Title: NMR Structure of the U3 RNA G-quadruplex
Authors: Marquevielle, J. / Amrane, S.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*CP*AP*GP*GP*GP*AP*GP*GP*UP*GP*UP*GP*GP*CP*CP*UP*GP*GP*GP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6643
Polymers7,5861
Non-polymers782
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
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: RNA chain RNA (5'-R(*CP*AP*GP*GP*GP*AP*GP*GP*UP*GP*UP*GP*GP*CP*CP*UP*GP*GP*GP*CP*GP*GP*G)-3')


Mass: 7585.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HIV-1 06TG.HT008 (virus)
#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
111isotropic12D NOESY
121isotropic32D 1H-1H TOCSY
131isotropic12D 1H-13C HSQC
141isotropic32D 1H-13C HMBC

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Sample preparation

DetailsType: solution / Contents: 1.5 mM 1H rHIVpro3, 90% H2O/10% D2O / Label: rHIVpro3 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mM / Component: rHIVpro3 / Isotopic labeling: 1H
Sample conditionsIonic strength: 35 mM / Label: buffer 1X / pH: 6.9 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO9501
Bruker AVANCE NEOBrukerAVANCE NEO7002
Bruker AVANCE NEOBrukerAVANCE NEO6003

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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: simulated annealing / 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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