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- PDB-8clr: Integrated NMR/MD structure determination of a dynamic and thermo... -

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Basic information

Entry
Database: PDB / ID: 8clr
TitleIntegrated NMR/MD structure determination of a dynamic and thermodynamically stable CUUG RNA tetraloop
ComponentsRNA hairpin with CUUG tetraloop
KeywordsRNA / Model Hairpin / Conformational Ensemble / MD / CUUG / Tetraloop / High Resolution
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic RNA (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsOxenfarth, A. / Kuemmerer, F. / Bottaro, S. / Schnieders, R. / Pinter, G. / Jonker, H.R.A. / Fuertig, B. / Richter, C. / Blackledge, M. / Lindorff-Larsen, K. / Schwalbe, H.
Funding support Germany, European Union, Denmark, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC902 Germany
European CommissioniNEXT-discoveryEuropean Union
LundbeckfondenR155-2015-2666 Denmark
Novo Nordisk FoundationNNF18OC0032608 Denmark
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Integrated NMR/Molecular Dynamics Determination of the Ensemble Conformation of a Thermodynamically Stable CUUG RNA Tetraloop.
Authors: Oxenfarth, A. / Kummerer, F. / Bottaro, S. / Schnieders, R. / Pinter, G. / Jonker, H.R.A. / Furtig, B. / Richter, C. / Blackledge, M. / Lindorff-Larsen, K. / Schwalbe, H.
History
DepositionFeb 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Data collection / Database references / Category: citation / citation_author / pdbx_validate_planes
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_validate_planes.type
Revision 1.2Aug 9, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 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 hairpin with CUUG tetraloop


Theoretical massNumber of molelcules
Total (without water)4,4551
Polymers4,4551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)100 / 20100target function
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA hairpin with CUUG tetraloop


Mass: 4454.683 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 14mer RNA hairpin with CUUG tetraloop / Source: (synth.) synthetic RNA (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic42D 1H-1H NOESY
137isotropic32D 1H-13C HSQC
126anisotropic32D 1H-13C HSQC
147isotropic32D 1H-15N HSQC
156anisotropic32D 1H-15N HSQC
162isotropic13D qHCP
172isotropic12D qHCP
182isotropic12D P-FIDS
192isotropic43D HCC-TOCSY-CCH-E.COSY
1101isotropic12D HNN-COSY
1112isotropic22D gamma (H)CCH
1122isotropic52D gamma HCNCH
1132isotropic12D gamma HCP
1142isotropic12D 1H-13C HSQC
1151isotropic12D 1H-15N HSQC
1161isotropic22D HCN
1172isotropic43D forward directed (H)CCH-TOCSY
1182isotropic13D HCP

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.64 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS, 95% H2O/5% D2O13C15N in H2O95% H2O/5% D2O
solution21.26 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS, 100% D2O13C15N in D2O100% D2O
solution30.98 mM RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS, 100% D2OUnlabeled in D2O100% D2O
solution40.86 mM RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS, 95% H2O/5% D2OUnlabeled in H2O95% H2O/5% D2O
solution70.2 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS, 95% H2O/5% D2OIsotropic in H2O95% H2O/5% D2O
solution60.2 mM [U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura RNA hairpin with CUUG tetraloop, 10 mM potassium phosphate, 1 mM EDTA, 50 uM DSS, 20 mg/mL Pf1 phage, 95% H2O/5% D2OAnisotropic in H2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.64 mMRNA hairpin with CUUG tetraloop[U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura1
10 mMpotassium phosphatenatural abundance1
1 mMEDTAnatural abundance1
50 uMDSSnatural abundance1
1.26 mMRNA hairpin with CUUG tetraloop[U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura2
10 mMpotassium phosphatenatural abundance2
1 mMEDTAnatural abundance2
50 uMDSSnatural abundance2
0.98 mMRNA hairpin with CUUG tetraloopnatural abundance3
10 mMpotassium phosphatenatural abundance3
1 mMEDTAnatural abundance3
50 uMDSSnatural abundance3
0.86 mMRNA hairpin with CUUG tetraloopnatural abundance4
10 mMpotassium phosphatenatural abundance4
1 mMEDTAnatural abundance4
50 uMDSSnatural abundance4
0.2 mMRNA hairpin with CUUG tetraloop[U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura7
10 mMpotassium phosphatenatural abundance7
1 mMEDTAnatural abundance7
50 uMDSSnatural abundance7
0.2 mMRNA hairpin with CUUG tetraloop[U-13C; U-15N]-Ade,-Cyt, -Gua, -Ura6
10 mMpotassium phosphatenatural abundance6
1 mMEDTAnatural abundance6
50 uMDSSnatural abundance6
20 mg/mLPf1 phagenatural abundance6
Sample conditionsIonic strength: 13 mM / Label: condition / pH: 6.4 / Pressure: ambient mbar / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001cryoprobe
Bruker AVANCE III HDBrukerAVANCE III HD7002cryoprobe
Bruker AVANCEBrukerAVANCE8003cryoprobe
Bruker AVANCEBrukerAVANCE9004cryoprobe
Bruker AVANCE IIBrukerAVANCE II6005cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyNMRFAMLee W, Tonelli M, Markley JL Goddard TD, and Kneller DGchemical shift assignment
SparkyNMRFAMLee W, Tonelli M, Markley JL Goddard TD, and Kneller DGpeak picking
GROMACShttps://www.gromacs.org/structure calculation
PALESZweckstetter and Baxdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 3
Details: MD simulations were refined using Bayesian/Maximum entropy reweighting using RDCs and 3J-couplings. The obtained weights were then used to sub-sample an ensemble of 100 structures. See ...Details: MD simulations were refined using Bayesian/Maximum entropy reweighting using RDCs and 3J-couplings. The obtained weights were then used to sub-sample an ensemble of 100 structures. See manuscript for more details.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20100 / Conformers submitted total number: 100

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