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- PDB-2gm0: Linear dimer of stemloop SL1 from HIV-1 -

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Basic information

Entry
Database: PDB / ID: 2gm0
TitleLinear dimer of stemloop SL1 from HIV-1
ComponentsRNA (35-MER)
KeywordsRNA / LINEAR DIMER / A-RICH INTERNAL LOOP / G-RICH INTERNAL LOOP
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Restrained Metropolis Monte Carlo, restrained minimization in helical parameter's space
AuthorsUlyanov, N.B. / Mujeeb, A. / Du, Z. / Tonelli, M. / Parslow, T.G. / James, T.L.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: NMR Structure of the Full-length Linear Dimer of Stem-Loop-1 RNA in the HIV-1 Dimer Initiation Site.
Authors: Ulyanov, N.B. / Mujeeb, A. / Du, Z. / Tonelli, M. / Parslow, T.G. / James, T.L.
History
DepositionApr 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 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: RNA (35-MER)
B: RNA (35-MER)


Theoretical massNumber of molelcules
Total (without water)22,7382
Polymers22,7382
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 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (35-MER)


Mass: 11368.844 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
2322D NOESY
1433D 13C-separated NOESY
155non-decoupled constant-time 1H-13C TROSY-HSQC
2642D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.75 mM unlabeled SL1 RNA, 10 mM potassium phosphate buffer, 250 mM NaCl, 0.1 mM MgCl2, pH 6.4, D2OD2O
20.75 mM unlabeled SL1 RNA, 10 mM potassium phosphate buffer, 250 mM NaCl, 0.1 mM MgCl2,pH 6.4, 90% H2O, 10% D2O90% H2O/10% D2O
30.75 mM of uniformly 13C, 15N-labeled SL1 RNA, 10 mM potassium phosphate buffer, 250 mM NaCl, 0.1 mM MgCl2, pH 6.4, D2OD2O
40.75 mM of uniformly 13C, 15N-labeled SL1 RNA, 10 mM potassium phosphate buffer, 250 mM NaCl, 0.1 mM MgCl2, pH 6.4, 90% H2O, 10% D2O90% H2O/10% D2O
50.75 mM of uniformly 13C, 15N-labeled SL1 RNA, 10 mM potassium phosphate buffer, 250 mM NaCl, 0.1 mM MgCl2, pH 6.4, filamentous phage Pf1, D2OD2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM potassium phosphate buffer, 250 mM NaCl, 0.1 mM Mg Cl2 6.4 ambient 303 K
210 mM potassium phosphate buffer, 250 mM NaCl, 0.1 mM Mg Cl2 6.4 ambient 288 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 INOVAVarianINOVA6001
Varian Unity InovaVarianUnity Inova9002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1collection
NMRPipe2.3Delaglioprocessing
MARDIGRAS3.21Borgias et aliterative matrix relaxation
Sparky3.11Goddarddata analysis
DYANA1.5Guntertrefinement
miniCarloZhurkin & Ulyanovrefinement
RefinementMethod: Restrained Metropolis Monte Carlo, restrained minimization in helical parameter's space
Software ordinal: 1
Details: The structures are determined based on a total of 842 restraints; 608 are NOE-derived distance restraints, 104 hydrogen bond restraints, and 130 residual dipolar coupling (RDC) restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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