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- PDB-9dll: NMR structures of small molecules bound to a model of an RNA CAG ... -

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Basic information

Entry
Database: PDB / ID: 9dll
TitleNMR structures of small molecules bound to a model of an RNA CAG repeat expansion.
ComponentsCAG 13-mer RNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3')
KeywordsRNA / CAG repeats / Huntingtons Disease / muscle blind-like 1
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: Nucleic Acids Res. / Year: 2024
Title: NMR structures of small molecules bound to a model of an RNA CAG repeat expansion.
Authors: Chen, J.L. / Taghavi, A. / Disney, M.D. / Fountain, M.A.
History
DepositionSep 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAG 13-mer RNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3')
B: CAG 13-mer RNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6253
Polymers8,3132
Non-polymers3121
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 CAG 13-mer RNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3')


Mass: 4156.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-A1AZM / 4-carbamimidamidophenyl 4-carbamimidamidobenzoate


Mass: 312.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16N6O2 / 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
232isotropic12D NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3'), 0.7 mM 4-guanidinophenyl 4-guanidinobenzoate, 5 mM potassium phosphate, 0.25 mM EDTA, 100% D2Osample_1100% D2O
solution20.7 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3'), 0.7 mM 4-guanidinophenyl 4-guanidinobenzoate, 5 mM potassium phosphate, 0.25 mM EDTA, 95% H2O/5% D2Osample_295% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMRNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3')natural abundance1
0.7 mM4-guanidinophenyl 4-guanidinobenzoatenatural abundance1
5 mMpotassium phosphatenatural abundance1
0.25 mMEDTAnatural abundance1
0.7 mMRNA (5'-R(*GP*AP*CP*AP*GP*CP*AP*GP*CP*UP*GP*UP*C)-3')natural abundance2
0.7 mM4-guanidinophenyl 4-guanidinobenzoatenatural abundance2
5 mMpotassium phosphatenatural abundance2
0.25 mMEDTAnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
15 mMcondition_161 atm298 K
25 mMcondition_261 atm279 K

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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
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
Amber20Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanstructure calculation
NMRFAM-SPARKY1.47Goddard TD & Kneller DG (2008) SPARKY 3. University of California, San Francisco.data analysis
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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