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- PDB-5lwj: Solution NMR structure of the GTP binding Class II RNA aptamer-li... -

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Basic information

Entry
Database: PDB / ID: 5lwj
TitleSolution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.
ComponentsGTP Class II RNA (34-MER)
KeywordsRNA / RNA structure / aptamer / protonated adenine / GTP
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (unknown)
MethodSOLUTION NMR / molecular dynamics
AuthorsWolter, A.C. / Weickhmann, A.K. / Nasiri, A.H. / Hantke, K. / Ohlenschlaeger, O. / Wunderlich, C.H. / Kreutz, C. / Duchardt-Ferner, E. / Woehnert, J.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationWO901/1-1 to J.W Germany
German Research FoundationCollaborative Research Center (SFB) 902 Molecular principles of RNA based regulation Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: A Stably Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP-Binding RNA Aptamer.
Authors: Wolter, A.C. / Weickhmann, A.K. / Nasiri, A.H. / Hantke, K. / Ohlenschlager, O. / Wunderlich, C.H. / Kreutz, C. / Duchardt-Ferner, E. / Wohnert, J.
History
DepositionSep 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2May 8, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: ndb_struct_na_base_pair / pdbx_audit_support / pdbx_nmr_software
Item: _ndb_struct_na_base_pair.hbond_type_12 / _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.3Sep 18, 2019Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP Class II RNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5402
Polymers11,0171
Non-polymers5231
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1070 Å2
ΔGint9 kcal/mol
Surface area6660 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1target function

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Components

#1: RNA chain GTP Class II RNA (34-MER)


Mass: 11016.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SELEX / Source: (synth.) synthetic construct (unknown)
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic52D 1H-1H NOESY
128isotropic63D 1H-13C NOESY aliphatic
1312isotropic53D 1H-13C NOESY aliphatic3D 1H-13C NOESY aliphatic
1410isotropic53D 1H-13C NOESY aliphatic
157isotropic52D 1H-13C NOESY aromatic
1611isotropic42D 2D 1H-13C NOESY aromatic
179isotropic53D 1H-13C NOESY aromatic
188isotropic23D (H)CCH-TOCSY
1912isotropic23D (H)CCH-TOCSY
11010isotropic23D (H)CCH-TOCSY
1118isotropic23D (H)CCH-COSY
11212isotropic23D (H)CCH-COSY
11310isotropic23D (H)CCH-COSY
2144isotropic22D 1H-15N HNN-COSY
11512isotropic62D 1H-13C HNCO
1169isotropic72D 1H-13C H5(6)C5(6)C4NH3
1179isotropic72D 1H-13C H5(6)C5(6)C4N4H4
1188isotropic22D 1H-15N HCN aromatic
11912isotropic22D 1H-15N HCN aromatic
12010isotropic62D 1H-15N HCN aromatic
1218isotropic22D 1H-15N HCN aliphatic
12212isotropic22D 1H-15N HCN aliphatic
12310isotropic62D 1H-15N HCN aliphatic
1244isotropic2D 1H-15N 2bond-HSQC
1258isotropic22D 1H-1H (H)CCH-TOCSY (adenine)
1268isotropic22D 1H-31P H(C)P
12712isotropic22D 1H-31P H(C)P
12810isotropic22D 1H-31P H(C)P
1292isotropic22D (H)CCH-COSY
13011isotropic22D 1H-13C long-rangeH8(C8)C5(N1)H1
1314isotropic62D CMPG NOESY
1322isotropic63D 1H-13C NOESY aliphatic
1331isotropic53D 1H-13C NOESY aromatic
13413isotropic2lr-2D-HNN-COSY
13513isotropic22D-HNN-COSY NH2
1368isotropic63D 13C-F1 filtered, 13C-F3-edited NOESY HSQC
13712isotropic53D 13C-F1 filtered, 13C-F3-edited NOESY HSQC
13810isotropic63D 13C-F1 filtered, 13C-F3-edited NOESY HSQC
2394isotropic22D 1H-15N HSQC
2404isotropic62D 1H-15N HSQC NH2 only
1416isotropic42D 1H-13C HSQC aromatic
1426isotropic62D 1H-13C HSQC aliphatic
1433isotropic62D 15N-F2 edited 1H,1H NOESY
1448isotropic23D (H)CCH-TOCSY-CCH-E.COSY
14510isotropic23D (H)CCH-TOCSY-CCH-E.COSY
14612isotropic23D (H)CCH-TOCSY-CCH-E.COSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.66 mM GTP Class II RNA (34-MER), 1.32 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O, 95% H2O/5% D2OGTP Cl II unlabeledRNAunl_H2O95% H2O/5% D2O
solution20.66 mM GTP Class II RNA (34-MER), 1.32 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O, 100% D2OGTP Cl II unlabeledRNA_unl_D2O100% D2O
solution30.9 mM GTP Class II RNA (34-MER), 1.8 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O, 95% H2O/5% D2OGTP Cl II unlabeledRNA_unl_H2O_295% H2O/5% D2O
solution40.5 mM [U-99% 15N] GTP Class II RNA (34-MER), 1 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium phosphate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O, 95% H2O/5% D2OGTP Cl II 15N uniformly labeled15N_RNA95% H2O/5% D2O
solution50.36 mM [U-99% 13C; U-99% 15N] GTP Class II RNA (34-MER), 0.72 mM GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 90 % H2O, 10 % D2O, 90% H2O/10% D2OGTP Cl II 13C15N uniformly labeled13C15N_RNA_H2O90% H2O/10% D2O
solution61.2 mM [U-99% 13C; U-99% 15N] GTP Class II RNA (34-MER), 2.4 mM GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O, 100% D2OGTP Cl II 13C15N uniformly labeled13C15NRNA_D2O100% D2O
solution71.1 mM [U-13C; U-15N]-Ade GTP Class II RNA (34-MER), 2.2 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O, 95% H2O/5% D2OGTP Cl II 13C15N-Ade labeledAde_H2O95% H2O/5% D2O
solution81.1 mM [U-13C; U-15N]-Ade GTP Class II RNA (34-MER), 2.2 mM [U-99% 13C; U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O, 100% D2OGTP Cl II 13C15N-Ade labeledAde_D2O100% D2O
solution90.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O, 95% H2O/5% D2OGTP Cl II 13C15N-Cyt labeledCyt_H2O95% H2O/5% D2O
solution100.73 mM [U-13C; U-15N]-Cyt GTP Class II RNA (34-MER), 1.46 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O, 100% D2OGTP Cl II 13C15N-Cyt labeledCyt_D2O100% D2O
solution110.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 25 mM H2O, 100 % D2O, 95% H2O/5% D2OGTP Cl II 13C15N-GuaUri labeledGU_H2O95% H2O/5% D2O
solution120.82 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura GTP Class II RNA (34-MER), 1.64 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 100 % D2O, 100% D2OGTP Cl II 13C15N-GuaUri labeledGU_D2O100% D2O
solution131.3 mM [U-15N]-Gua, [U-15N]-Ade GTP Class II RNA (34-MER), 2.6 mM [U-99% 15N] GTP, 2 mM magnesium acetate, 25 mM potassium phosphate, 25 mM potassium chloride, 95 % H2O, 5 % D2O, 95% H2O/5% D2OGTP Cl II 15N-GuaAde labeled15N-G/A95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.66 mMGTP Class II RNA (34-MER)natural abundance1
1.32 mMGTP[U-99% 13C; U-99% 15N]1
2 mMmagnesium acetatenatural abundance1
25 mMpotassium phosphatenatural abundance1
25 mMpotassium chloridenatural abundance1
95 %H2Onatural abundance1
5 %D2Onatural abundance1
0.66 mMGTP Class II RNA (34-MER)natural abundance2
1.32 mMGTP[U-99% 13C; U-99% 15N]2
2 mMmagnesium acetatenatural abundance2
25 mMpotassium phosphatenatural abundance2
25 mMpotassium chloridenatural abundance2
100 %D2Onatural abundance2
0.9 mMGTP Class II RNA (34-MER)natural abundance3
1.8 mMGTP[U-99% 13C; U-99% 15N]3
2 mMmagnesium acetatenatural abundance3
25 mMpotassium phosphatenatural abundance3
25 mMpotassium chloridenatural abundance3
95 %H2Onatural abundance3
5 %D2Onatural abundance3
0.5 mMGTP Class II RNA (34-MER)[U-99% 15N]4
1 mMGTP[U-99% 13C; U-99% 15N]4
2 mMmagnesium phosphatenatural abundance4
25 mMpotassium phosphatenatural abundance4
25 mMpotassium chloridenatural abundance4
95 %H2Onatural abundance4
5 %D2Onatural abundance4
0.36 mMGTP Class II RNA (34-MER)[U-99% 13C; U-99% 15N]5
0.72 mMGTPnatural abundance5
2 mMmagnesium acetatenatural abundance5
25 mMpotassium phosphatenatural abundance5
25 mMpotassium chloridenatural abundance5
90 %H2Onatural abundance5
10 %D2Onatural abundance5
1.2 mMGTP Class II RNA (34-MER)[U-99% 13C; U-99% 15N]6
2.4 mMGTPnatural abundance6
2 mMmagnesium acetatenatural abundance6
25 mMpotassium phosphatenatural abundance6
25 mMpotassium chloridenatural abundance6
100 %D2Onatural abundance6
1.1 mMGTP Class II RNA (34-MER)[U-13C; U-15N]-Ade7
2.2 mMGTP[U-99% 13C; U-99% 15N]7
2 mMmagnesium acetatenatural abundance7
25 mMpotassium phosphatenatural abundance7
25 mMpotassium chloridenatural abundance7
95 %H2Onatural abundance7
5 %D2Onatural abundance7
1.1 mMGTP Class II RNA (34-MER)[U-13C; U-15N]-Ade8
2.2 mMGTP[U-99% 13C; U-99% 15N]8
2 mMmagnesium acetatenatural abundance8
25 mMpotassium phosphatenatural abundance8
25 mMpotassium chloridenatural abundance8
100 %D2Onatural abundance8
0.73 mMGTP Class II RNA (34-MER)[U-13C; U-15N]-Cyt9
1.46 mMGTP[U-99% 15N]9
2 mMmagnesium acetatenatural abundance9
25 mMpotassium phosphatenatural abundance9
25 mMpotassium chloridenatural abundance9
95 %H2Onatural abundance9
5 %D2Onatural abundance9
0.73 mMGTP Class II RNA (34-MER)[U-13C; U-15N]-Cyt10
1.46 mMGTP[U-99% 15N]10
2 mMmagnesium acetatenatural abundance10
25 mMpotassium phosphatenatural abundance10
25 mMpotassium chloridenatural abundance10
100 %D2Onatural abundance10
0.82 mMGTP Class II RNA (34-MER)[U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura11
1.64 mMGTP[U-99% 15N]11
2 mMmagnesium acetatenatural abundance11
25 mMpotassium phosphatenatural abundance11
25 mMpotassium chloridenatural abundance11
25 mMH2Onatural abundance11
100 %D2Onatural abundance11
0.82 mMGTP Class II RNA (34-MER)[U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura12
1.64 mMGTP[U-99% 15N]12
2 mMmagnesium acetatenatural abundance12
25 mMpotassium phosphatenatural abundance12
25 mMpotassium chloridenatural abundance12
100 %D2Onatural abundance12
1.3 mMGTP Class II RNA (34-MER)[U-15N]-Gua, [U-15N]-Ade13
2.6 mMGTP[U-99% 15N]13
2 mMmagnesium acetatenatural abundance13
25 mMpotassium phosphatenatural abundance13
25 mMpotassium chloridenatural abundance13
95 %H2Onatural abundance13
5 %D2Onatural abundance13
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (Pa)Temperature (K)
1standard NMR-buffer pH 6.3, 293 Kpotassium chloride (25) mMconditions_16.3 1 atm293 K
2standard NMR-buffer pH 6.3, 283 Kpotassium chloride (25) mMconditions_26.3 1 atm283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6002cryogenic probehead
Bruker AVANCEBrukerAVANCE7007cryogenic probehead
Bruker AVANCEBrukerAVANCE8006cryogenic probehead
Bruker AVANCEBrukerAVANCE9005cryogenic probehead
Bruker AVANCEBrukerAVANCE9504cryogenic probehead

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
TopSpin3.5Bruker Biospinprocessing
TopSpin3.5Bruker Biospindata analysis
CARA1.8.4.2Keller and Wuthrichchemical shift assignment
CARA1.8.4.2Keller and Wuthrichpeak picking
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
OPALLuginbuhl, Guntert, Billeter, Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 9
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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