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- PDB-1n8x: Solution structure of HIV-1 Stem Loop SL1 -

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Basic information

Entry
Database: PDB / ID: 1n8x
TitleSolution structure of HIV-1 Stem Loop SL1
ComponentsHIV-1 STEM LOOP SL1 MONOMERIC RNA
KeywordsRNA / HIV / SL1 / RNA STEM LOOP / BULGE / G-A MISMATCH
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING
AuthorsLawrence, D.C. / Stover, C.C. / Noznitsky, J. / Wu, Z. / Summers, M.F.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structure of the Intact Stem and Bulge of HIV-1 Psi-RNA Stem-Loop SL1
Authors: Lawrence, D.C. / Stover, C.C. / Noznitsky, J. / Wu, Z. / Summers, M.F.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE Author states there are three additional bases on the 5' and 3' ends, which form WC base ...SEQUENCE Author states there are three additional bases on the 5' and 3' ends, which form WC base pairs: 5'-GGA ... UCC-3' DIS loop (AAGCGCGCA) replaced with GAGA tetraloop' Monomeric RNA engineered by replacing the terminal loop with a GAGA tetraloop. Lower stem has an additional three base pairs: 5'GGA...UCC3'. Residues are numbered 1 through 36 in coordinate file although they are numbered differently in article. Internal bulged loop composed of G5 (5' strand), A24, G25, and G26 (3' strand) is structured with a G5-A24 mismatch and G25, G26 stacking under A24.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 STEM LOOP SL1 MONOMERIC RNA


Theoretical massNumber of molelcules
Total (without water)11,7151
Polymers11,7151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 600target function
RepresentativeModel #1lowest target function

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Components

#1: RNA chain HIV-1 STEM LOOP SL1 MONOMERIC RNA


Mass: 11715.034 Da / Num. of mol.: 1 / Fragment: HIV-1 Stem Loop SL1 / Source method: obtained synthetically
Details: This sequence was synthesized by in vitro transcription using a single stranded DNA template and T7 RNA polymerase.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1214D 13C-separated NOESY
1313D 13C-separated ROESY
1423D 13C-separated NOESY
1524D 13C-separated NOESY
1633D 13C-separated NOESY
1734D 13C-separated NOESY
284IPAP H-COUPLED CT-HSQC
1952D NOESY
11052D ROESY
NMR detailsText: EXPERIMENT 8 (IPAP H-COUPLED CT-HSQC) WAS PERFORMED ON SAMPLE 4 AND SAMPLE 6 (GUA-15N,13C-LABELED SL1 WITH AND WITHOUT PF1 PHAGE). THE DIFFERENCE BETWEEN THE J-COUPLING VALUES = DIPOLAR ...Text: EXPERIMENT 8 (IPAP H-COUPLED CT-HSQC) WAS PERFORMED ON SAMPLE 4 AND SAMPLE 6 (GUA-15N,13C-LABELED SL1 WITH AND WITHOUT PF1 PHAGE). THE DIFFERENCE BETWEEN THE J-COUPLING VALUES = DIPOLAR COUPLING VALUE FOR A GIVEN C-H BOND.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM SL1 monomeric RNA, U-15N,13C; 100% D2O100% D2O
21 mM SL1 monomeric RNA, Cyt-15N,13C; 100% D2O100% D2O
31 mM SL1 monomeric RNA, Gua-15N,13C; 100% D2O100% D2O
41 mM SL1 monomeric RNA, Gua-15N,13C; 10 mM Tris-d11, pH 8.0, 0.1 mM EDTA; 18 mg/ml Pf1 bacteriophage (ASLA); 100% D2O100% D2O
51 mM SL1 monomeric RNA, unlabeled; 100% D2O100% D2O
61 mM SL1 monomeric RNA, Gua-15N,13C; 10 mM Tris-d11, pH 8.0, 0.1 mM EDTA; 100% D2O100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)Ionic strength
17.0 ambient 308 K
28.0 ambient 308 K10 mM Tris-Cl, 0.1 mM Na-EDTA
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
NMRView5.0.3Johnson, Blevinsdata analysis
DYANA1.5Guntert, Mumenthaler, Wuthrichrefinement
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
Details: The structures are based on a total of 408 experimental restraints, including 298 NOE-derived distance restraints, 84 hydrogen bond restraints, and 26 dipolar coupling restraints.
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 600 / Conformers submitted total number: 20

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