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- PDB-7qb3: Solution structure of a lanthanide-binding DNA aptamer -

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Basic information

Entry
Database: PDB / ID: 7qb3
TitleSolution structure of a lanthanide-binding DNA aptamer
ComponentsLanthanide-binding aptamer
KeywordsDNA / aptamer / lanthanide
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsAndralojc, W. / Gdaniec, Z.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science Centre2020/37/B/ST4/03182 Poland
Polish National Science Centre2018/31/D/ST4/01467 Poland
CitationJournal: Chemistry / Year: 2022
Title: Solution Structure of a Lanthanide-binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints.
Authors: Andralojc, W. / Wieruszewska, J. / Pasternak, K. / Gdaniec, Z.
History
DepositionNov 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
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

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lanthanide-binding aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8182
Polymers8,6431
Non-polymers1751
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, The geometry of the DNA-metal interaction was determined using paramagnetic NMR data: pseudo-contact shifts (PCS)
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: DNA chain Lanthanide-binding aptamer


Mass: 8642.544 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-LU / LUTETIUM (III) ION / LU


Mass: 174.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Lu / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-31P COSY
152isotropic12D 1H-1H NOESY
162isotropic12D 1H-13C HSQC
172isotropic12D 1H-1H TOCSY
182isotropic12D 1H-31P COSY
193isotropic12D NOESY
1103isotropic12D 1H-13C HSQC
1113isotropic12D 1H-1H TOCSY
1123isotropic12D 1H-31P COSY
1134isotropic12D NOESY
1144isotropic12D 1H-13C HSQC
1164isotropic12D 1H-1H TOCSY
1174isotropic12D 1H-31P COSY
1185isotropic12D NOESY
1195isotropic12D 1H-13C HSQC
1205isotropic12D 1H-1H TOCSY
1215isotropic12D 1H-31P COSY
1226isotropic12D NOESY
1236isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1700 uM Lanthanide-binding aptamer, 10 mM cacodylate, 150 mM sodium chloride, 700 uM Lutetium chloride, 100% D2OLu100% D2O
solution2700 uM Lanthanide-binding aptamer, 10 mM cacodylate, 150 mM sodium chloride, 700 uM Europium chloride, 100% D2OEu100% D2O
solution3700 uM Lanthanide-binding aptamer, 10 mM cacodylate, 150 mM sodium chloride, 700 uM Ytterbium acetate, 100% D2OYb100% D2O
solution4700 uM Lanthanide-binding aptamer, 10 mM cacodylate, 150 mM sodium chloride, 700 uM cerium chloride, 100% D2OCe100% D2O
solution5700 uM Lanthanide-binding aptamer, 10 mM cacodylate, 150 mM sodium chloride, 700 uM thulium chloride, 100% D2OTm100% D2O
solution6700 uM Lanthanide-binding aptamer, 10 mM cacodylate, 150 mM sodium chloride, 700 uM Lutetium chloride, 90% H2O/10% D2OLu_H2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
700 uMLanthanide-binding aptamernatural abundance1
10 mMcacodylatenatural abundance1
150 mMsodium chloridenatural abundance1
700 uMLutetium chloridenatural abundance1
700 uMLanthanide-binding aptamernatural abundance2
10 mMcacodylatenatural abundance2
150 mMsodium chloridenatural abundance2
700 uMEuropium chloridenatural abundance2
700 uMLanthanide-binding aptamernatural abundance3
10 mMcacodylatenatural abundance3
150 mMsodium chloridenatural abundance3
700 uMYtterbium acetatenatural abundance3
700 uMLanthanide-binding aptamernatural abundance4
10 mMcacodylatenatural abundance4
150 mMsodium chloridenatural abundance4
700 uMcerium chloridenatural abundance4
700 uMLanthanide-binding aptamernatural abundance5
10 mMcacodylatenatural abundance5
150 mMsodium chloridenatural abundance5
700 uMthulium chloridenatural abundance5
700 uMLanthanide-binding aptamernatural abundance6
10 mMcacodylatenatural abundance6
150 mMsodium chloridenatural abundance6
700 uMLutetium chloridenatural abundance6
Sample conditions

Ionic strength: 0.16 M / pH: 6.2 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K

Conditions-IDLabelDetails
2conditions_1
3conditions_2Eu

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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
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
NMRFAM-SPARKYNMRFAMchemical shift assignment
NMRFAM-SPARKYNMRFAMpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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