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- PDB-9cpi: Structures of small molecules bound to RNA repeat expansions that... -

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Basic information

Entry
Database: PDB / ID: 9cpi
TitleStructures of small molecules bound to RNA repeat expansions that cause Huntington's disease-like 2 and myotonic dystrophy type 1
ComponentsRNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3')
KeywordsRNA / CUG repeats / myotonic dystrophy type 1 / DM1 / 5'CUG/3'GUC
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, J.L. / Taghavi, A. / Disney, M.D. / Fountain, M.A. / Childs-Disney, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35 NS116846 United States
Department of Defense (DOD, United States)HT94252310336 United States
National Institutes of Health/Office of the DirectorS10-OD021550 United States
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2024
Title: NMR structures of small molecules bound to a model of a CUG RNA repeat expansion.
Authors: Chen, J.L. / Taghavi, A. / Frank, A.J. / Fountain, M.A. / Choudhary, S. / Roy, S. / Childs-Disney, J.L. / Disney, M.D.
History
DepositionJul 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3')
B: RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6433
Polymers8,2672
Non-polymers3761
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

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


Mass: 4133.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-A1AZL / 4-[1-(2-aminoethyl)-4,5-dihydro-1H-imidazol-2-yl]-N-[4-(4,5-dihydro-1H-imidazol-2-yl)phenyl]benzamide


Mass: 376.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N6O / 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 DQF-COSY
232isotropic22D NOESY
342isotropic22D NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.3 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-ium, 5 mM potassium phosphate, 0.25 mM EDTA, 100% D2Osample_1100% D2O
solution20.3 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-ium, 5 mM potassium phosphate, 0.25 mM EDTA, 95% H2O/5% D2Osample_295% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMRNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3')natural abundance1
0.6 mM1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-iumnatural abundance1
5 mMpotassium phosphatenatural abundance1
0.25 mMEDTAnatural abundance1
0.3 mMRNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3')natural abundance2
0.6 mM1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-iumnatural abundance2
5 mMpotassium phosphatenatural abundance2
0.25 mMEDTAnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
15 mMcondition_161 atm308 K
210 mMcondition_261 atm278 K
35 mMcondition_361 atm288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD7001
Bruker AVANCE III HDBrukerAVANCE III HD8502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospinprocessing
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanstructure calculation
NMRFAM-SPARKY1.3Bioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12 NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Lee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKY1.3Bioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12 NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Lee W, Tonelli M, Markley JLpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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