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- PDB-5kh8: Solution structures of the apo state fluoride riboswitch -

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Basic information

Entry
Database: PDB / ID: 5kh8
TitleSolution structures of the apo state fluoride riboswitch
Componentsriboswitch (47-MER)
KeywordsRNA / apo state / pseudoknot / riboswitch aptamer / transcriptional regulation
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR
AuthorsZhang, Q. / Zhao, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM114432 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: An excited state underlies gene regulation of a transcriptional riboswitch.
Authors: Zhao, B. / Guffy, S.L. / Williams, B. / Zhang, Q.
History
DepositionJun 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 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 1.6May 15, 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

Downloads & links

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Assembly

Deposited unit
A: riboswitch (47-MER)


Theoretical massNumber of molelcules
Total (without water)15,0541
Polymers15,0541
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
RepresentativeModel #1lowest energy

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Components

#1: RNA chain riboswitch (47-MER)


Mass: 15053.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) 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
211isotropic12D 1H-1H NOESY
122isotropic12D 1H-1H NOESY
132isotropic12D 1H-1H TOCSY
243isotropic12D 1H-15N HSQC
253isotropic12D 1H-13C HSQC
174isotropic12D 1H-13C HSQC
165isotropic12D 1H-13C HSQC
196isotropic12D 1H-13C HSQC
185isotropic12D (H)CCH COSY
1106isotropic12D (H)CCH COSY
1145isotropic13D (H)CCH-TOCSY
1136isotropic13D (H)CCH-TOCSY
1125isotropic231P spin-echo
1116isotropic231P spin-echo
1165isotropic2CH-(H)CCH spin-echo
1186isotropic2CH-(H)CCH spin-echo
1173anisotropic12D 1H-15N HSQC
1153anisotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM RNA (47mer), 10 mM magnesium chloride, 10 mM sodium phosphate, 50 mM potassium chloride, 50 uM EDTA, 95% H2O/5% D2OUnlabeled H2O95% H2O/5% D2O
solution21.0 mM RNA (47mer), 10 mM magnesium chloride, 10 mM sodium phosphate, 50 mM potassium chloride, 50 uM EDTA, 100% D2OUnlabeled D2O100% D2O
solution31.0 mM [U-100% 13C; U-100% 15N] RNA (47mer), 10 mM magnesium chloride, 10 mM sodium phosphate, 50 mM potassium chloride, 50 uM EDTA, 95% H2O/5% D2OFully labeled H2O95% H2O/5% D2O
solution41.0 mM [U-100% 13C; U-100% 15N] RNA (47mer), 10 mM magnesium chloride, 10 mM sodium phosphate, 50 mM potassium chloride, 50 uM EDTA, 100% D2OFully labeled D2O100% D2O
solution51.0 mM [U-13C; U-15N]-Gua RNA (47mer), 10 mM magnesium chloride, 10 mM sodium phosphate, 50 mM potassium chloride, 50 uM EDTA, 100% D2OG labeled D2O100% D2O
solution61.0 mM [U-13C; U-15N]-Ade ;[U-13C; U-15N]-Ura RNA (47mer), 10 mM magnesium chloride, 10 mM sodium phosphate, 50 mM potassium chloride, 50 uM EDTA, 100% D2OAU labeled D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRNA (47mer)natural abundance1
10 mMmagnesium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
50 mMpotassium chloridenatural abundance1
50 uMEDTAnatural abundance1
1.0 mMRNA (47mer)natural abundance2
10 mMmagnesium chloridenatural abundance2
10 mMsodium phosphatenatural abundance2
50 mMpotassium chloridenatural abundance2
50 uMEDTAnatural abundance2
1.0 mMRNA (47mer)[U-100% 13C; U-100% 15N]3
10 mMmagnesium chloridenatural abundance3
10 mMsodium phosphatenatural abundance3
50 mMpotassium chloridenatural abundance3
50 uMEDTAnatural abundance3
1.0 mMRNA (47mer)[U-100% 13C; U-100% 15N]4
10 mMmagnesium chloridenatural abundance4
10 mMsodium phosphatenatural abundance4
50 mMpotassium chloridenatural abundance4
50 uMEDTAnatural abundance4
1.0 mMRNA (47mer)[U-13C; U-15N]-Gua5
10 mMmagnesium chloridenatural abundance5
10 mMsodium phosphatenatural abundance5
50 mMpotassium chloridenatural abundance5
50 uMEDTAnatural abundance5
1.0 mMRNA (47mer)[U-13C; U-15N]-Ade ;[U-13C; U-15N]-Ura6
10 mMmagnesium chloridenatural abundance6
10 mMsodium phosphatenatural abundance6
50 mMpotassium chloridenatural abundance6
50 uMEDTAnatural abundance6
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
180 mM303K6.4 ambient atm303 K
280 mM283K6.4 ambient atm283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III5002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
TopSpin3.2Bruker Biospindata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
Sparky3.11Goddarddata analysis
Sparky3.11Goddardpeak picking
Sparky3.11Goddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers submitted total number: 20

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