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- PDB-2l94: Structure of the HIV-1 frameshift site RNA bound to a small molec... -

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Basic information

Entry
Database: PDB / ID: 2l94
TitleStructure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication
ComponentsRNA_(45-MER)
KeywordsRNA/INHIBITOR / RNA / Inhibitor / RNA-INHIBITOR complex
Function / homologyChem-L94 / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsMarcheschi, R.J. / Tonelli, M. / Kumar, A. / Butcher, S.E.
CitationJournal: Acs Chem.Biol. / Year: 2011
Title: Structure of the HIV-1 Frameshift Site RNA Bound to a Small Molecule Inhibitor of Viral Replication.
Authors: Marcheschi, R.J. / Tonelli, M. / Kumar, A. / Butcher, S.E.
History
DepositionJan 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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
A: RNA_(45-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8562
Polymers14,5201
Non-polymers3371
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA_(45-MER)


Mass: 14519.708 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-L94 / N'-{(Z)-amino[4-(amino{[3-(dimethylammonio)propyl]iminio}methyl)phenyl]methylidene}-N,N-dimethylpropane-1,3-diaminium


Mass: 336.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36N6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2222D 1H-1H NOESY
2322D 1H-1H TOCSY
2432D 1H-13C HSQC
2542D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.75 mM RNA (45-MER), 0.75 mM DB213, 20 uM DSS, 20 mM potassium chloride, 10 mM [U-2H] TRIS, 90% H2O/10% D2O90% H2O/10% D2O
20.75 mM RNA (45-MER), 0.75 mM DB213, 20 uM DSS, 20 mM potassium chloride, 10 mM [U-2H] TRIS, 100% D2O100% D2O
31.5 mM RNA (45-MER), 1.5 mM DB213, 40 uM DSS, 40 mM potassium chloride, 20 mM [U-2H] TRIS, 100% D2O100% D2O
41.5 mM RNA (45-MER), 1.5 mM DB213, 40 uM DSS, 40 mM potassium chloride, 20 mM [U-2H] TRIS, 4.5 mg Pf1 phage, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMRNA (45-MER)-11
0.75 mMDB213-21
20 uMDSS-31
20 mMpotassium chloride-41
10 mMTRIS-5[U-2H]1
0.75 mMRNA (45-MER)-62
0.75 mMDB213-72
20 uMDSS-82
20 mMpotassium chloride-92
10 mMTRIS-10[U-2H]2
1.5 mMRNA (45-MER)-113
1.5 mMDB213-123
40 uMDSS-133
40 mMpotassium chloride-143
20 mMTRIS-15[U-2H]3
1.5 mMRNA (45-MER)-164
1.5 mMDB213-174
40 uMDSS-184
40 mMpotassium chloride-194
20 mMTRIS-20[U-2H]4
4.5 mg/mLPf1 phage-214
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 7.0 ambient atm283 K
220 7.0 ambient atm308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Varian AvanceVarianAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
HADDOCK2Alexandre Bonvin, Utrecht Universitydocking
HADDOCK2Alexandre Bonvin, Utrecht Universityrefinement
HADDOCK2Alexandre Bonvin, Utrecht Universitystructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
SYBYL8Triposdata analysis
SYBYL8Triposgeometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
VnmrJVariancollection
PALESMarkus Zweckstetter, Ad Baxdata analysis
PyMOLDeLano Scientificdata analysis
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR constraintsNA chi-angle constraints total count: 45 / NA sugar pucker constraints total count: 78 / NOE constraints total: 786 / NOE intraresidue total count: 321 / NOE sequential total count: 369 / Hydrogen bond constraints total count: 96
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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