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- PDB-2kwg: Solution structure of a fully modified 2'-F/2'-OMe siRNA construct -

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Basic information

Entry
Database: PDB / ID: 2kwg
TitleSolution structure of a fully modified 2'-F/2'-OMe siRNA construct
Components
  • 5'-R(*(GF2)P*(OMG)P*(GF2)P*(OMU)P*(AF2)P*(A2M)P*(AF2)P*(OMU)P*(AF2)P*(OMC)P*(AF2)P*(OMU)P*(UFT)P*(OMC)P*(UFT)P*(OMU)P*(CFZ)P*(A2M)P*(UFT)P*(OMU)P*(UFT))-3'
  • 5'-R(P*(A2M)P*(UFT)P*(OMG)P*(AF2)P*(A2M)P*(GF2)P*(A2M)P*(AF2)P*(OMU)P*(GF2)P*(OMU)P*(AF2)P*(OMU)P*(UFT)P*(OMU)P*(AF2)P*(OMC)P*(CFZ)P*(OMC)P*(UFT)P*(OMU))-3'
KeywordsRNA / siRNA / 2'-fluoro / 2'-O-methyl
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPodbevsek, P. / Bhat, B. / Plavec, J.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Solution-state structure of a fully alternately 2'-F/2'-OMe modified 42-nt dimeric siRNA construct.
Authors: Podbevsek, P. / Allerson, C.R. / Bhat, B. / Plavec, J.
History
DepositionApr 9, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*(GF2)P*(OMG)P*(GF2)P*(OMU)P*(AF2)P*(A2M)P*(AF2)P*(OMU)P*(AF2)P*(OMC)P*(AF2)P*(OMU)P*(UFT)P*(OMC)P*(UFT)P*(OMU)P*(CFZ)P*(A2M)P*(UFT)P*(OMU)P*(UFT))-3'
B: 5'-R(P*(A2M)P*(UFT)P*(OMG)P*(AF2)P*(A2M)P*(GF2)P*(A2M)P*(AF2)P*(OMU)P*(GF2)P*(OMU)P*(AF2)P*(OMU)P*(UFT)P*(OMU)P*(AF2)P*(OMC)P*(CFZ)P*(OMC)P*(UFT)P*(OMU))-3'


Theoretical massNumber of molelcules
Total (without water)13,6332
Polymers13,6332
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 5'-R(*(GF2)P*(OMG)P*(GF2)P*(OMU)P*(AF2)P*(A2M)P*(AF2)P*(OMU)P*(AF2)P*(OMC)P*(AF2)P*(OMU)P*(UFT)P*(OMC)P*(UFT)P*(OMU)P*(CFZ)P*(A2M)P*(UFT)P*(OMU)P*(UFT))-3'


Mass: 6799.100 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(P*(A2M)P*(UFT)P*(OMG)P*(AF2)P*(A2M)P*(GF2)P*(A2M)P*(AF2)P*(OMU)P*(GF2)P*(OMU)P*(AF2)P*(OMU)P*(UFT)P*(OMU)P*(AF2)P*(OMC)P*(CFZ)P*(OMC)P*(UFT)P*(OMU))-3'


Mass: 6834.176 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1322D 1H-1H NOESY
2412D 1H-1H NOESY
2522D 1H-1H NOESY
1612D HP-COSY
1712D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM RNA-1, 2 mM RNA-2, 100% D2O100% D2O
22 mM RNA-1, 2 mM RNA-2, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2 mMISIS401156-11
2 mMISIS401157-21
2 mMISIS401156-32
2 mMISIS401157-42
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1206.8ambient 25 K
2206.8ambient 5 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Uniform NMR SystemVarianUniform NMR System8001
Varian Uniform NMR SystemVarianUniform NMR System6002

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.115Goddardchemical shift assignment
VnmrJ2.2CVariancollection
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 100 ps of NMR restrained simulated annealing calculations using a generalized Born implicit solvation model.
NMR constraintsNA alpha-angle constraints total count: 33 / NA beta-angle constraints total count: 33 / NA chi-angle constraints total count: 42 / NA delta-angle constraints total count: 42 / NA epsilon-angle constraints total count: 33 / NA other-angle constraints total count: 67
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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