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- PDB-6i1v: Structure of the RNA duplex containing pseudouridine residue (5'-... -

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Basic information

Entry
Database: PDB / ID: 6i1v
TitleStructure of the RNA duplex containing pseudouridine residue (5'-Cp(PSU)pG-3' sequence context)
Components
  • RNA (5'-R(*AP*CP*UP*CP*AP*GP*UP*GP*A)-3')
  • RNA (5'-R(*UP*CP*AP*CP*(PSU)P*GP*AP*GP*U)-3')
KeywordsRNA / duplex / pseudouridine
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsDeb, I. / Popenda, L. / Sarzynska, J. / Gdaniec, Z.
Funding support Poland, Italy, 3items
OrganizationGrant numberCountry
UMO-2017/25/B/ST5/00971 Poland
S/IND 15-05 Italy
UMO-2013/08/A/ST5/00295 Poland
CitationJournal: Sci Rep / Year: 2019
Title: Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair.
Authors: Deb, I. / Popenda, L. / Sarzynska, J. / Malgowska, M. / Lahiri, A. / Gdaniec, Z. / Kierzek, R.
History
DepositionOct 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,6882
Polymers5,6882
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1420 Å2
ΔGint0 kcal/mol
Surface area3430 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 2832.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(*AP*CP*UP*CP*AP*GP*UP*GP*A)-3')


Mass: 2855.767 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
111isotropic12D 1H-1H NOESY
221isotropic12D 1H-1H NOESY
332isotropic12D 1H-1H NOESY
141isotropic12D DQF-COSY
151isotropic12D 1H-13C HSQC
161isotropic12D 1H-13C HSQC aliphatic
171isotropic12D 1H-31P COSY
181isotropic12D 1H-31P HETERO TOCSY-NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM pUCAC(PSU)GAGU, 0.5 mM pACUCAGUGA, 10 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 100% D2Oseq_f_D2O100% D2O
solution20.5 mM pUCAC(PSU)GAGU, 0.5 mM pACUCAGUGA, 10 mM sodium phosphate, 150 mM sodium chloride, 0.1 mM EDTA, 90% H2O/10% D2Oseq_f_H2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMpUCAC(PSU)GAGUnatural abundance1
0.5 mMpACUCAGUGAnatural abundance1
10 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
0.1 mMEDTAnatural abundance1
0.5 mMpUCAC(PSU)GAGUnatural abundance2
0.5 mMpACUCAGUGAnatural abundance2
10 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
0.1 mMEDTAnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10.16 M25C6.8ambient atm298 K
20.16 M35C6.8ambient atm308 K
30.16 M15C6.8ambient atm288 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
FelixAccelrys Software Inc.peak picking
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.data analysis
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Refinement
MethodSoftware ordinal
simulated annealing6
simulated annealing7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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