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- PDB-7q6l: Solution structure of an intramolecular RNA G-quadruplex formed b... -

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Entry
Database: PDB / ID: 7q6l
TitleSolution structure of an intramolecular RNA G-quadruplex formed by the 6A8A17U mutant from a 22mer guanine-rich sequence within the 5'UTR of BCL-2 proto-oncogene
ComponentsRNA (5'-R(*GP*GP*GP*CP*CP*AP*UP*AP*GP*GP*GP*UP*GP*GP*GP*AP*UP*CP*UP*GP*GP*G)-3')
KeywordsRNA / G-quadruplex / BCL-2 / mRNA / 5'UTR / intramolecular
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, Z. / Jurt, S. / Dominguez-Martin, A. / Johannsen, S. / Sigel, R.K.O.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation165868 Switzerland
University of ZurichFK-14-100, FK-15-096 Switzerland
CitationJournal: To Be Published
Title: Solution structure of an intramolecular RNA G-quadruplex formed by the 6A8A17U mutant from a 22mer guanine-rich sequence within the 5'UTR of BCL-2 proto-oncogene
Authors: Wang, Z. / Jurt, S. / Dominguez-Martin, A. / Johannsen, S. / Sigel, R.K.O.
History
DepositionNov 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 2, 2025Group: Database references / Experimental preparation / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_nmr_details
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(*GP*GP*GP*CP*CP*AP*UP*AP*GP*GP*GP*UP*GP*GP*GP*AP*UP*CP*UP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,2251
Polymers7,2251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7225.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-1H NOESY
222isotropic22D 1H-1H NOESY
232isotropic22D 1H-1H TOCSY
242isotropic22D 1H-13C HSQC
151isotropic1JR-HMBC
363isotropic2H8N2 HNN-COSY
373isotropic2H1N2 HNN-COSY
282isotropic1H1pC6/8 HMBC
494isotropic1constant-time 1H-13C HSQC
5105isotropic1constant-time 1H-13C HSQC
6116isotropic1constant-time 1H-13C HSQC
7127isotropic1constant-time 1H-13C HSQC
NMR detailsText: In this structure the 5' triphosphate moiety is not included, due to the lack of structural information that can be gathered by NMR, leaving a 5'-hydroxyl end.

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.3 mM BCL-2 6A8A17U, 90% H2O/10% D2O1.3 mM RNA, 2.0 mM KCl, 90/10% H2O/D2O, pH=7BCL-2 6A8A17U mutant_H2O90% H2O/10% D2O
solution21.3 mM BCL-2 6A8A17U, 100% D2O1.3 mM RNA, 2.0 mM KCl, 100% D2O, pH=7BCL-2 6A8A17U mutant_D2O100% D2O
solution30.5 mM G 15N-labeled BCL-2 6A8A17U, 90% H2O/10% D2O0.5 mM RNA with G 15N-labeled, 2.0 mM KCl, 90/10% H2O/D2O, pH=7BCL-2 6A8A17U mutant G 15N-labeled_H2O90% H2O/10% D2O
solution40.3 mM A 13C, 15N-labeled BCL-2 6A8A17U, 100% D2O0.3 mM RNA with A 13C, 15N-labeled, 2.0 mM KCl, 100% D2O, pH=7BCL-2 6A8A17U mutant A 13C, 15N-labeled_D2O100% D2O
solution50.3 mM C 13C, 15N-labeled BCL-2 6A8A17U, 100% D2O0.3 mM RNA with C 13C, 15N-labeled, 2.0 mM KCl, 100% D2O, pH=7BCL-2 6A8A17U mutant C 13C, 15N-labeled_D2O100% D2O
solution60.5 mM G 13C-labeled BCL-2 6A8A17U, 100% D2O0.5 mM RNA with G 13C-labeled, 2.0 mM KCl, 100% D2O, pH=7BCL-2 6A8A17U mutant G 13C-labeled_D2O100% D2O
solution70.3 mM U 13C, 15N-labeled BCL-2 6A8A17U, 100% D2O0.3 mM RNA with U 13C, 15N-labeled, 2.0 mM KCl, 100% D2O, pH=7BCL-2 6A8A17U mutant U 13C, 15N-labeled_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMBCL-2 6A8A17Unatural abundance1
1.3 mMBCL-2 6A8A17Unatural abundance2
0.5 mMBCL-2 6A8A17UG 15N-labeled3
0.3 mMBCL-2 6A8A17UA 13C, 15N-labeled4
0.3 mMBCL-2 6A8A17UC 13C, 15N-labeled5
0.5 mMBCL-2 6A8A17UG 13C-labeled6
0.3 mMBCL-2 6A8A17UU 13C, 15N-labeled7
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
12 mMexchangeable71 atm298 K
22 mMnon-exchangeable71 atm298 K
32 mMhydrogen bond71 atm298 K
42 mMconstant-time HSQC of A71 atm298 K
52 mMconstant-time HSQC of C71 atm298 K
62 mMconstant-time HSQC of G71 atm298 K
72 mMconstant-time HSQC of U71 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001Cryo-TCI
Bruker AVANCEBrukerAVANCE7002Cryo-TXI

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.0.6Bruker Biospincollection
NMRFAM-SPARKY1.414Lee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKY1.414Lee W, Tonelli M, Markley JLpeak picking
X-PLOR NIH3Schwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIH3Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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