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- PDB-6ge1: Solution structure of the r(UGGUGGU)4 RNA quadruplex -

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Basic information

Entry
Database: PDB / ID: 6ge1
TitleSolution structure of the r(UGGUGGU)4 RNA quadruplex
ComponentsRNA (5'-R(*UP*GP*GP*UP*GP*GP*U)-3')
KeywordsRNA / quadruplex / tetramolecular / parallel stranded / U-tetrad
Function / homologyRNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics / simulated annealing
AuthorsAndralojc, W. / Gdaniec, Z.
Funding support Poland, 2items
OrganizationGrant numberCountry
National Science CenterUMO-2014/13/B/ST5/04144 Poland
National Science CenterUMO-2013/08/A/ST5/00295 Poland
CitationJournal: RNA / Year: 2019
Title: Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus.
Authors: Andralojc, W. / Malgowska, M. / Sarzynska, J. / Pasternak, K. / Szpotkowski, K. / Kierzek, R. / Gdaniec, Z.
History
DepositionApr 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
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 (5'-R(*UP*GP*GP*UP*GP*GP*U)-3')
B: RNA (5'-R(*UP*GP*GP*UP*GP*GP*U)-3')
C: RNA (5'-R(*UP*GP*GP*UP*GP*GP*U)-3')
D: RNA (5'-R(*UP*GP*GP*UP*GP*GP*U)-3')


Theoretical massNumber of molelcules
Total (without water)9,0174
Polymers9,0174
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3150 Å2
ΔGint-62 kcal/mol
Surface area3750 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 400target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 2254.363 Da / Num. of mol.: 4 / 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
321isotropic12D 1H-1H NOESY
232isotropic12D 1H-1H NOESY
242isotropic12D 1H-1H TOCSY
351isotropic12D 1H-13C HSQC
361isotropic12D 1H-31P COSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride, 100% D2OUGG_KCl_D2O100% D2O
solution22.0 mM pUGGUGGU, 10 mM phosphate buffer, 0.05 mM potassium chloride, 90% H2O/10% D2OUGG_KCl_H2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMpUGGUGGUnatural abundance1
10 mMphosphate buffernatural abundance1
50 mMpotassium chloridenatural abundance1
2.0 mMpUGGUGGUnatural abundance2
10 mMphosphate buffernatural abundance2
0.05 mMpotassium chloridenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10.06 M25C6.81 atm298 K
20.06 M5C6.81 atm278 K
30.06 M55C6.81 bar333 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
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
Refinement
MethodSoftware ordinal
molecular dynamics1
simulated annealing2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 15

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