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- PDB-6hyk: NMR solution structure of the C/D box snoRNA U14 -

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Basic information

Entry
Database: PDB / ID: 6hyk
TitleNMR solution structure of the C/D box snoRNA U14
ComponentsRNA (31-MER)
KeywordsRNA / snoRNA / U14 / K-turn / Snu13p
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChagot, M.E. / Quinternet, M. / Rothe, B. / Charpentier, B. / Coutant, J. / Manival, X. / Lebars, I.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-16-CE11-0032-02 France
CitationJournal: Biochimie / Year: 2019
Title: The yeast C/D box snoRNA U14 adopts a "weak" K-turn like conformation recognized by the Snu13 core protein in solution.
Authors: Chagot, M.E. / Quinternet, M. / Rothe, B. / Charpentier, B. / Coutant, J. / Manival, X. / Lebars, I.
History
DepositionOct 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Jun 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 (31-MER)


Theoretical massNumber of molelcules
Total (without water)9,9991
Polymers9,9991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6170 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: RNA chain RNA (31-MER)


Mass: 9998.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
221isotropic12D 1H-1H NOESY
431isotropic12D 1H-1H NOESY
141isotropic12D 1H-15N HSQC
251isotropic12D 1H-15N HSQC
461isotropic12D 1H-15N HSQC
471isotropic12D 1H-13C HSQC
681anisotropic12D 1H-15N HSQC
1161isotropic12D HNN COSY
2171isotropic12D HNN COSY
3181isotropic12D HNN COSY
392isotropic12D 1H-1H NOESY
4102isotropic12D 1H-1H NOESY
5112isotropic12D 1H-1H NOESY
3122isotropic12D MLEV
4132isotropic12D MLEV
5142isotropic12D MLEV
3152isotropic12D 1H-13C HSQC
4192isotropic12D 1H-13C HSQC
5202isotropic12D 1H-13C HSQC
6212anisotropic12D 1H-13C HSQC
4222isotropic12D DQF-COSY
4232isotropic12D HCN
4242isotropic13D (H)CCH-TOCSY
4252isotropic23D HCP
4262isotropic22D HPCOSY
4272isotropic22D HCC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1500 uM RNA (31-MER), 500 uM [U-99% 13C; U-99% 15N] RNA (31-MER), 90% H2O/10% D2O50 mM sodium phosphate buffer pH6.4 150 mM NaClU14_H2O90% H2O/10% D2O
solution2500 uM RNA (31-MER), 500 uM [U-99% 13C; U-99% 15N] RNA (31-MER), 100% D2O50 mM sodium phosphate buffer pH6.4 150 mM NaClU14_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMRNA (31-MER)_unlabelnatural abundance1
500 uMRNA (31-MER)_label[U-99% 13C; U-99% 15N]1
500 uMRNA (31-MER)_unlabelnatural abundance2
500 uMRNA (31-MER)_label[U-99% 13C; U-99% 15N]2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mM sodium phosphate buffer pH6.4 150 mM NaCl150 mM NaCl Not definedconditions_16.4 atmospheric Pa283 K
250 mM sodium phosphate buffer pH6.4 150 mM NaCl150 mM NaCl Not definedconditions_26.4 ambient Pa288 K
350 mM sodium phosphate buffer pH6.4 150 mM NaCl150 mM NaCl Not definedconditions_36.4 ambient Pa293 K
450 mM sodium phosphate buffer pH6.4 150 mM NaCl150 mM NaCl Mconditions_46.4 ambient Pa298 K
550 mM sodium phosphate buffer pH6.4 150 mM NaCl150 mM NaCl Not definedcondition_56.4 ambient Pa303 K
650 mM sodium phosphate buffer pH6.4 150 mM NaCl pf1 filamentous bacteriophage150 mM NaCl Not definedconditions_66.4 ambient Pa298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCE NEOBrukerAVANCE NEO5002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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