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- PDB-9eow: The 5-terminal stem-loop RNA element of SARS-CoV-2 features highl... -

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Basic information

Entry
Database: PDB / ID: 9eow
TitleThe 5-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH
ComponentsRNA (29-MER)
KeywordsRNA / solution structure / conformational dynamics / PkA shift / adenosine protonation
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodSOLUTION NMR / simulated annealing
AuthorsWacker, A. / Schwalbe, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)495006306 Germany
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH.
Authors: Toews, S. / Wacker, A. / Faison, E.M. / Duchardt-Ferner, E. / Richter, C. / Mathieu, D. / Bottaro, S. / Zhang, Q. / Schwalbe, H.
History
DepositionMar 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (29-MER)


Theoretical massNumber of molelcules
Total (without water)9,2051
Polymers9,2051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (29-MER)


Mass: 9204.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: GenBank: NC_045512

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic21H-JR[15N]
121isotropic1NOESY[15N]-Imino
131isotropic2HSQC[15N]-Amino
141isotropic2HSQC[15N]-2J
151isotropic2TROSY[15N]
1161isotropic2NOESY-JR[15N]-Amino
1151isotropic2TOCSY
2142isotropic2HSQC[13C]-Aromaten
2132isotropic21H-JR[15N]
2122isotropic2NOESY[15N]-Imino
2112isotropic1HSQC[15N]-Amino
2102isotropic2HSQC[15N]-2J
292isotropic2TROSY[15N]
282isotropic1NOESY-JR[15N]-Amino
272isotropic3TOCSY
262isotropic2HSQC[13C]-Aromaten
3173isotropic3HSQC[13C]-Aromaten

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1150 uM [U-15N] 5_SL1 15N, 25 mM potassium phosphate, 50 mM KCl, 93% H2O/7% D2O5_SL193% H2O/7% D2O
solution2400 uM [U-13C; U-15N] 5_SL1 15N, 25 mM potassium phosphate, 50 mM KCl, 93% H2O/7% D2O5_SL193% H2O/7% D2O
solution3400 uM A,C-13C, U-15N 5_SL1 15N, 25 mM potassium phosphate, 50 mM KCl, 93% H2O/7% D2O5_SL193% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 uM5_SL1 15N[U-15N]1
25 mMpotassium phosphatenatural abundance1
50 mMKClnatural abundance1
400 uM5_SL1 15N[U-13C; U-15N]2
25 mMpotassium phosphatenatural abundance2
50 mMKClnatural abundance2
400 uM5_SL1 15NA,C-13C, U-15N3
25 mMpotassium phosphatenatural abundance3
50 mMKClnatural abundance3
Sample conditions

Ionic strength: 75 mM / Ionic strength err: 1 / pH: 6.2 / Pressure: 1 atm

Conditions-IDLabelPH errTemperature (K)
15_SL1 13C 15N 283K0.1283 K
25_SL1 13C 15N 298K0.1298 K
35_SL1 13C 15N 298K1.5298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Bruker Avance III HD 800BrukerBruker Avance III HD 800 8001
Bruker Bruker Avance III HD 700BrukerBruker Avance III HD 700 7002
Bruker Bruker Avance I 600BrukerBruker Avance I 600 6003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
NMRFAM-SPARKYWonghee Leepeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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