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- PDB-5vh7: Structure and dynamics of RNA repeat expansions that cause Huntin... -

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Basic information

Entry
Database: PDB / ID: 5vh7
TitleStructure and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1
ComponentsRNA (5'-R(*GP*AP*CP*CP*AP*GP*CP*AP*G)-3')
KeywordsRNA / CAG repeat / triplet repeat / Huntington's Disease / repeat expansion / AA pair
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, J.L. / VanEtten, D.M. / Fountain, M.A. / Yildirim, I. / Disney, M.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)DP1NS096898 United States
Muscular Dystrophy Association380467 United States
CitationJournal: Biochemistry / Year: 2017
Title: Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1.
Authors: Chen, J.L. / VanEtten, D.M. / Fountain, M.A. / Yildirim, I. / Disney, M.D.
History
DepositionApr 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*AP*CP*CP*AP*GP*CP*AP*G)-3')
B: RNA (5'-R(*GP*AP*CP*CP*AP*GP*CP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)9,6602
Polymers9,6602
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 4829.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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
232isotropic22D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM NA Adenosine, Cytidine,Guanosine, Uridine RNA (5'-R(*GP*AP*CP*CP*AP*GP*CP*AP*G)-3'), 5.0 mM potassium phosphate, 0.25 mM EDTA, 100% D2O0.5 mM ribonucleic acid, 5 mM KH2PO4/K2HPO4, 0.25 mM EDTASample 100% D2O100% D2O
solution20.5 mM NA Adenosine, Cytidine,Guanosine, Uridine RNA (5'-R(*GP*AP*CP*CP*AP*GP*CP*AP*G)-3'), 5.0 mM potassium phosphate, 0.25 mM EDTA, 95% H2O/5% D2O0.5 mM ribonucleic acid, 5 mM KH2PO4/K2HPO4, 0.25 mM EDTASample 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMRNA (5'-R(*GP*AP*CP*CP*AP*GP*CP*AP*G)-3')NA Adenosine, Cytidine,Guanosine, Uridine1
5.0 mMpotassium phosphatenatural abundance1
0.25 mMEDTAnatural abundance1
0.5 mMRNA (5'-R(*GP*AP*CP*CP*AP*GP*CP*AP*G)-3')NA Adenosine, Cytidine,Guanosine, Uridine2
5.0 mMpotassium phosphatenatural abundance2
0.25 mMEDTAnatural abundance2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
10.5 mM ribonucleic acid, 5 mM KH2PO4/K2HPO4, 0.25 mM EDTA0.0112 MCondition 100% D2O6 1 atm298 K
20.5 mM ribonucleic acid, 5 mM KH2PO4/K2HPO4, 0.25 mM EDTA0.0112 MCondition 95% H2O/5% D2O6 1 atm278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance III HD UltraShieldBrukerAvance III HD UltraShield7001
Bruker Avance III HD AscendBrukerAvance III HD Ascend8502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.5Bruker Biospincollection
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
Sparky3Goddardchemical shift assignment
Sparky3Goddardpeak picking
Amber16Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmandata analysis
NMRPipe8.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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