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- PDB-7pof: Structural effects of m6A modification of the Xist A repeat AUCG ... -

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Entry
Database: PDB / ID: 7pof
TitleStructural effects of m6A modification of the Xist A repeat AUCG tetraloop and its recognition by YTHDC1
ComponentsRNA (5'-R(*GP*GP*CP*GP*CP*(6MZ)P*UP*CP*GP*GP*CP*GP*CP*C)-3')
KeywordsRNA / Xist / lncRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsJones, A.N. / Sattler, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1309-325871075 Germany
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1.
Authors: Jones, A.N. / Tikhaia, E. / Mourao, A. / Sattler, M.
History
DepositionSep 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 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

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*CP*GP*CP*(6MZ)P*UP*CP*GP*GP*CP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,5071
Polymers4,5071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area600 Å2
ΔGint1 kcal/mol
Surface area2780 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (5'-R(*GP*GP*CP*GP*CP*(6MZ)P*UP*CP*GP*GP*CP*GP*CP*C)-3')


Mass: 4506.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
132isotropic22D 1H-1H NOESY
111isotropic22D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
143isotropic12D HNN COSY
153isotropic23D 1H-13C NOESY HMQC
163isotropic22D 1H-13C HMQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution125 mM sodium chloride, 25 mM sodium phosphate, 100% D2OD2O unlabeled (m6A)UCG tetraloop sample 1100% D2O
solution225 mM sodium chloride, 25 mM sodium phosphate, 95% H2O/5% D2OH2O unlabeled (m6A)UCG tetraloop sample 295% H2O/5% D2O
solution325 mM sodium chloride, 25 mM sodium phosphate, 100% D2OU 13C 15N (m6A)UCG tetraloop sample 2100% D2O6MZ is unlabeled
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium chloridenatural abundance1
25 mMsodium phosphatenatural abundance1
25 mMsodium chloridenatural abundance2
25 mMsodium phosphatenatural abundance2
25 mMsodium chloridenatural abundance3
25 mMsodium phosphatenatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
125 mM298 K6.51 atm298 K
225 mM298 K6.51 atm298 K
325 mM298 K6.51 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III9501cryoprobe
Bruker AVANCE IIIBrukerAVANCE III9002cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4CCPNchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TopSpin3.5 pl6Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10

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