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- PDB-2ktz: Inhibitor Induced Structural Change in the HCV IRES Domain IIa RNA -

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Basic information

Entry
Database: PDB / ID: 2ktz
TitleInhibitor Induced Structural Change in the HCV IRES Domain IIa RNA
ComponentsHCV IRES Domain IIa RNA
KeywordsRNA / Hepatitis C Virus / RNA Structure / Antiviral
Function / homologyChem-ISH / RNA / RNA (> 10)
Function and homology information
Biological speciesHepatitis C virus
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 7
AuthorsPaulsen, R.B. / Seth, P.P. / Swayze, E.E. / Griffey, R.H. / Skalicky, J.J. / Cheatham III, T.E. / Davis, D.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Inhibitor-induced structural change in the HCV IRES domain IIa RNA.
Authors: Paulsen, R.B. / Seth, P.P. / Swayze, E.E. / Griffey, R.H. / Skalicky, J.J. / Cheatham, T.E. / Davis, D.R.
History
DepositionFeb 10, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HCV IRES Domain IIa RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4402
Polymers12,1221
Non-polymers3171
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 16structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain HCV IRES Domain IIa RNA


Mass: 12122.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 polymerase / Source: (synth.) Hepatitis C virus
#2: Chemical ChemComp-ISH / (7R)-7-[(dimethylamino)methyl]-1-[3-(dimethylamino)propyl]-7,8-dihydro-1H-furo[3,2-e]benzimidazol-2-amine


Mass: 317.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N5O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
3232D 1H-15N HSQC
1322D 1H-13C HSQC
1412D 1H-1H TOCSY
1542D (H)CCH COSY
1642D 1H-1H F1fF2f-NOESY
1742D 1H-1H F1fF2e-NOESY
2842D 1H-13C HSQC-IPAP
2942D (H)CCH COSY-IPAP
11052D 1H-1H F1fF2f-NOESY
11152D 1H-1H F1fF2e-NOESY
11242D 1H-13C HSQC
11352D 1H-13C HSQC
21452D 1H-13C HSQC-IPAP
21552D (H)CCH COSY-IPAP
11652D (H)CCH COSY
11722D 1H-1H F1fF2e-NOESY
31832D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
1400 uM RNA (38-MER)-1, 150 mM sodium chloride-2, 150 mM potassium chloride-3, 10 mM sodium phosphate-4, 2 mM spermine-5, 2.8 mM ISH-6, 100% D2O100% D2O
2.4 mM [U-100% 13C; U-100% 15N] RNA (38-MER)-7, 150 mM sodium chloride-8, 150 mM potassium chloride-9, 10 mM sodium phosphate-10, 2 mM spermine-11, 2.8 mM ISH-12, 100% D2O100% D2O
3.4 mM [U-100% 13C; U-100% 15N] RNA (38-MER)-13, 150 mM sodium chloride-14, 150 mM potassium chloride-15, 10 mM sodium phosphate-16, 2 mM spermine-17, 2.8 mM ISH-18, 90% H2O/10% D2O90% H2O/10% D2O
4.4 mM [U-13C; U-15N]-Ura, Ade RNA (38-MER)-19, 150 mM sodium chloride-20, 150 mM potassium chloride-21, 10 mM sodium phosphate-22, 2 mM spermine-23, 2.8 mM ISH-24, 100% D2O100% D2O
5.4 mM [U-13C; U-15N]-Gua, Cyt RNA (38-MER)-25, 150 mM sodium chloride-26, 150 mM potassium chloride-27, 10 mM sodium phosphate-28, 2 mM spermine-29, 2.8 mM ISH-30, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMRNA (38-MER)-11
150 mMsodium chloride-21
150 mMpotassium chloride-31
10 mMsodium phosphate-41
2 mMspermine-51
2.8 mMISH-61
.4 mMRNA (38-MER)-7[U-100% 13C; U-100% 15N]2
150 mMsodium chloride-82
150 mMpotassium chloride-92
10 mMsodium phosphate-102
2 mMspermine-112
2.8 mMISH-122
.4 mMRNA (38-MER)-13[U-100% 13C; U-100% 15N]3
150 mMsodium chloride-143
150 mMpotassium chloride-153
10 mMsodium phosphate-163
2 mMspermine-173
2.8 mMISH-183
.4 mMRNA (38-MER)-19[U-13C; U-15N]-Ura, Ade4
150 mMsodium chloride-204
150 mMpotassium chloride-214
10 mMsodium phosphate-224
2 mMspermine-234
2.8 mMISH-244
.4 mMRNA (38-MER)-25[U-13C; U-15N]-Gua, Cyt5
150 mMsodium chloride-265
150 mMpotassium chloride-275
10 mMsodium phosphate-285
2 mMspermine-295
2.8 mMISH-305
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.150 NaCl 7 ambient 308 K
20.150 NaCl 7 ambient 304 K
30.150 NaCl 7 ambient 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR softwareName: Amber / Version: 10
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 16 / Conformers submitted total number: 10

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