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- PDB-5xi1: Structural Insight of Flavonoids binding to CAG repeat RNA that c... -

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Basic information

Entry
Database: PDB / ID: 5xi1
TitleStructural Insight of Flavonoids binding to CAG repeat RNA that causes Huntington's Disease (HD) and Spinocerebellar Ataxia (SCAs)
ComponentsRNA (5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3')
KeywordsRNA / Myricetin / Flavonoids / CAG RNA / HD / Huntington's Disease / Trinucleotide repeats
Function / homologyChem-MYC / RNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTawani, A. / Mishra, S.K. / Khan, E. / Kumar, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science and Technology, Government of IndiaSR/FT/LS-29/2012 India
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Myricetin Reduces Toxic Level of CAG Repeats RNA in Huntington's Disease (HD) and Spino Cerebellar Ataxia (SCAs).
Authors: Khan, E. / Tawani, A. / Mishra, S.K. / Verma, A.K. / Upadhyay, A. / Kumar, M. / Sandhir, R. / Mishra, A. / Kumar, A.
History
DepositionApr 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 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
S: RNA (5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3')
A: RNA (5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4084
Polymers5,7722
Non-polymers6362
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1940 Å2
ΔGint-6 kcal/mol
Surface area3590 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 2885.799 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-MYC / 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE / 2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE / 3,3',4',5,5',7-HEXAHYDROXYFLAVONE / MYRICETIN / CANNABISCETIN / Myricetin


Mass: 318.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
211anisotropic12D NOESY
221anisotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 1.54 mM RNA (5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3'), 3.08 mM MYC, 90% H2O/10% D2O
Label: na / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.54 mMRNA (5'-R(P*CP*CP*GP*CP*AP*GP*CP*GP*G)-3')1
3.08 mMMYC1
Sample conditionsDetails: with 50 mM NaCl / Ionic strength: 10 mM / Label: Sodium phosphate Buffer / pH: 7.2 / Pressure: 760 mmHg / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospinchemical shift assignment
DiscoverAccelrys Software Inc.refinement
TopSpinBruker Biospinprocessing
SparkyGoddardprocessing
RefinementMethod: simulated annealing / Software ordinal: 2 / Details: 9 intermolecular restrainst
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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