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- PDB-2f4x: NMR Solution of HIV-1 Lai Kissing Complex -

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Basic information

Entry
Database: PDB / ID: 2f4x
TitleNMR Solution of HIV-1 Lai Kissing Complex
Components5'-R(P*GP*GP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*C)-3'
KeywordsRNA / SL1 / kissing complex / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsKieken, F. / Paquet, F. / Brule, F. / Paoletti, J. / Lancelot, G.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: A new NMR solution structure of the SL1 HIV-1Lai loop-loop dimer
Authors: Kieken, F. / Paquet, F. / Brule, F. / Paoletti, J. / Lancelot, G.
History
DepositionNov 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 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: 5'-R(P*GP*GP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*C)-3'
B: 5'-R(P*GP*GP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)15,5252
Polymers15,5252
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)18 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7762.693 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF COSY
2422D NOESY
2522D TOCSY
262DQF COSY
272PFG
183HSQC
193HCN
1103HMBC
1113(H)CCH TOCSY
112313C, 15N half filter

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Sample preparation

Details
Solution-IDContentsSolvent system
1unlabeled sample, 2 mM, 90% H2O, 10% D2O90% H2O/10% D2O
2unlabeled sample, 2 mM, 100% D2O100% D2O
315N,13C labeled sample, 0.6 mM, 90% H2O, 10% D2O90% H2O/10% D2O
415N,13C labeled sample, 0.6 mM, 100% D2O100% D2O
5mixture of unlabeled sample and a 15N,13C labeled sample, 0.6 mM, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1none 6atmospheric atm283 K
2none 6atmospheric atm288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY6001
Varian UNITYVarianUNITY8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVarianprocessing
NMRPipe5.0.3Delaglioprocessing
CNS1.1Brungerrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 18

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