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- PDB-2l6i: Solution structure of coronaviral stem-loop 2 (SL2) -

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Basic information

Entry
Database: PDB / ID: 2l6i
TitleSolution structure of coronaviral stem-loop 2 (SL2)
ComponentsRNA (5'-R(*GP*AP*UP*CP*UP*CP*UP*UP*GP*UP*AP*GP*AP*UP*CP*A)-3')
KeywordsRNA / RNA tetraloop / severe acute respiratory syndrome / mouse hepatitis virus / coronavirus
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, molecular dynamics
AuthorsLee, C. / Li, L. / Giedroc, D.P.
CitationJournal: Febs Lett. / Year: 2011
Title: The solution structure of coronaviral stem-loop 2 (SL2) reveals a canonical CUYG tetraloop fold.
Authors: Lee, C.W. / Li, L. / Giedroc, D.P.
History
DepositionNov 21, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

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MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,0601
Polymers5,0601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)27 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (5'-R(*GP*AP*UP*CP*UP*CP*UP*UP*GP*UP*AP*GP*AP*UP*CP*A)-3')


Mass: 5060.023 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-13C HSQC
1413D (H)CCH-TOCSY
1512D HNCCCH
1612D H(CCN)H-TOCSY
1712D HCN-HMQC
1812D HCN-TROSY
1912D HCNCH
2122D 1H-1H NOESY
2222D 1H-1H TOCSY
2322D 1H-13C HSQC
2423D (H)CCH-TOCSY
2522D HNCCCH
2622D H(CCN)H-TOCSY
2722D HCN-HMQC
2822D HCN-TROSY
2922D HCNCH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-2 mM SL2, 0.8-2 mM [U-13C; U-15N]-Ura SL2, 10 mM potassium phosphate, 0.1 mM DSS, 90%H2O/10%D2O90% H2O/10% D2O
20.8-2 mM SL2, 0.8-2 mM [U-13C; U-15N]-Ura SL2, 10 mM potassium phosphate, 0.1 mM DSS, 100%D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMSL20.8-21
mM13C,15N SL2[U-13C; U-15N]-Ura0.8-21
10 mMpotassium phosphate1
0.1 mMDSS1
mMSL20.8-22
mM13C,15N SL2[U-13C; U-15N]-Ura0.8-22
10 mMpotassium phosphate2
0.1 mMDSS2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
106ambient 283 K
206ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 27

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