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- PDB-7rwr: An RNA aptamer that decreases flavin redox potential -

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Basic information

Entry
Database: PDB / ID: 7rwr
TitleAn RNA aptamer that decreases flavin redox potential
ComponentsRNA (38-MER)
KeywordsRNA / RNA aptamer
Function / homologyFLAVIN MONONUCLEOTIDE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsGremminger, T. / Li, J. / Chen, S. / Heng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Aeronautic Space Administration (NASA, United States)NNX17AE88G United States
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: An RNA aptamer that shifts the reduction potential of metabolic cofactors.
Authors: Samuelian, J.S. / Gremminger, T.J. / Song, Z. / Poudyal, R.R. / Li, J. / Zhou, Y. / Staller, S.A. / Carballo, J.A. / Roychowdhury-Saha, M. / Chen, S.J. / Burke, D.H. / Heng, X. / Baum, D.A.
History
DepositionAug 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 28, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 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 (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6912
Polymers12,2341
Non-polymers4561
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, Kd=191 +/- 66 nM
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (38-MER)


Mass: 12234.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / 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 1H-1H NOESY
122isotropic12D 1H-1H NOESY
133isotropic12D 1H-1H NOESY
144isotropic12D 1H-1H NOESY
155isotropic12D 1H-1H NOESY
161isotropic12D 1H-1H COSY
276isotropic1HNN-COSY
2107isotropic1HNN-COSY
186isotropic1F1fF2f-NOESY
196isotropic1F2f-NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1300 uM U-1H RNA (38-MER), 300 uM U-1H FMN, 100% D2OTx041-FMN100% D2O
solution2300 uM A-H, C-D, G-H, U-D RNA (38-MER), 300 uM U-1H FMN, 100% D2OAG-Tx041-FMN100% D2O
solution3300 uM A-H, C-H, G-D, U-D RNA (38-MER), 300 uM U-1H FMN, 100% D2OAC-Tx041-FMN100% D2O
solution4300 uM A-D, C-D, G-H, U-H RNA (38-MER), 300 uM U-H FMN, 100% D2OGU-Tx041-FMN100% D2O
solution5300 uM A-8D, C-H, G-H, U-5,6D2 RNA (38-MER), 300 uM U-1H FMN, 100% D2OA2rUrGC-Tx041-FMN100% D2O
solution6300 uM [U-100% 13C; U-100% 15N] RNA (38-MER), 300 uM U-1H FMN, 90% H2O/10% D2O13C/15N-Tx041-FMN90% H2O/10% D2O
solution7300 uM [U-100% 13C; U-100% 15N] RNA (38-MER), 300 uM dioxopyrimidine-13C4, 15N2 FMN, 90% H2O/10% D2O13C/15N-Tx041-13C/15N-FMN90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMRNA (38-MER)U-1H1
300 uMFMNU-1H1
300 uMRNA (38-MER)A-H, C-D, G-H, U-D2
300 uMFMNU-1H2
300 uMRNA (38-MER)A-H, C-H, G-D, U-D3
300 uMFMNU-1H3
300 uMRNA (38-MER)A-D, C-D, G-H, U-H4
300 uMFMNU-H4
300 uMRNA (38-MER)A-8D, C-H, G-H, U-5,6D25
300 uMFMNU-1H5
300 uMRNA (38-MER)[U-100% 13C; U-100% 15N]6
300 uMFMNU-1H6
300 uMRNA (38-MER)[U-100% 13C; U-100% 15N]7
300 uMFMNdioxopyrimidine-13C4, 15N27
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
120 mM MgCl2 mM308K7.51 atm308 K
220 mM MgCl2 mM283K6.51 atm283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJJohnsonchemical shift assignment
NMRViewJJohnsonpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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