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- PDB-1bvj: HIV-1 RNA A-RICH HAIRPIN LOOP -

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Basic information

Entry
Database: PDB / ID: 1bvj
TitleHIV-1 RNA A-RICH HAIRPIN LOOP
ComponentsRNA (5'-R(P*GP*GP*CP*GP*AP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*AP*UP*CP*UP*CP*GP*CP* C)-3')
KeywordsRNA / HIV-1 GENOMIC RNA / REVERSE TRANSCRIPTASE INITIATION / RNA HAIRPIN LOOP
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus type 1
MethodSOLUTION NMR / simulated annealing
AuthorsPuglisi, E.V. / Puglisi, J.D.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: HIV-1 A-rich RNA loop mimics the tRNA anticodon structure.
Authors: Puglisi, E.V. / Puglisi, J.D.
History
DepositionAug 31, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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 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: RNA (5'-R(P*GP*GP*CP*GP*AP*CP*GP*GP*UP*GP*UP*AP*AP*AP*AP*AP*UP*CP*UP*CP*GP*CP* C)-3')


Theoretical massNumber of molelcules
Total (without water)7,4021
Polymers7,4021
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)21 / 160LOWEST TOTAL AND RESTRAINT VIOLATION ENERGIES
RepresentativeModel #14

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Components

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


Mass: 7402.472 Da / Num. of mol.: 1 / Fragment: A-RICH HAIRPIN LOOP / Source method: isolated from a natural source
Source: (natural) Human immunodeficiency virus type 1 (MAL ISOLATE)
Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: MAL ISOLATE / References: GenBank: AF096656

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY 2D
131COSY 3D
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE HCN AND HCP EXPERIMENTS ON 15N,13C-LABELED RNA.

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Sample preparation

Sample conditionsIonic strength: 10mM NA PHOSPHATE / pH: 6.4 / Temperature: 283 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRCHITECTMSIrefinement
MSI NMRCHITECTNMRCHITECTstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: SEE REFERENCE ABOVE
NMR ensembleConformer selection criteria: LOWEST TOTAL AND RESTRAINT VIOLATION ENERGIES
Conformers calculated total number: 160 / Conformers submitted total number: 21

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