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- PDB-1bau: NMR STRUCTURE OF THE DIMER INITIATION COMPLEX OF HIV-1 GENOMIC RN... -

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Basic information

Entry
Database: PDB / ID: 1bau
TitleNMR STRUCTURE OF THE DIMER INITIATION COMPLEX OF HIV-1 GENOMIC RNA, MINIMIZED AVERAGE STRUCTURE
ComponentsSL1 RNA DIMER
KeywordsRNA / RIBONUCLEIC ACID / HIV-1 / DIMERIZATION / ENCAPSIDATION
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR
AuthorsMujeeb, A. / Clever, J.L. / Billeci, T.M. / James, T.L. / Parslow, T.G.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Structure of the dimer initiation complex of HIV-1 genomic RNA.
Authors: Mujeeb, A. / Clever, J.L. / Billeci, T.M. / James, T.L. / Parslow, T.G.
History
DepositionApr 18, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
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: SL1 RNA DIMER
B: SL1 RNA DIMER


Theoretical massNumber of molelcules
Total (without water)14,8352
Polymers14,8352
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)1 / 34LOWEST NMR CONSTRAINT VIOLATIONS AND LOWEST AMBER ENERGY.
Representative

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Components

#1: RNA chain SL1 RNA DIMER


Mass: 7417.488 Da / Num. of mol.: 2 / Fragment: HIV-1 PACKAGING SIGNAL, RESIDUE 248-270 / Source method: obtained synthetically / Details: RNA SYNTHESIZED USING T7 RNA TRANSCRIPTION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOE IN D2O
1212D NOE IN WATER
131DQF-COSY
NMR detailsText: INTERPROTON-DISTANCE INFORMATION (IN THE FORM OF NOE CROSS-PEAKS) WAS COLLECTED FROM 2D NOE EXPERIMENTS IN D2O AS WELL AS IN 90% H2O FOR NON-EXCHANGEABLE AND EXCHANGEABLE PROTONS, RESPECTIVELY. ...Text: INTERPROTON-DISTANCE INFORMATION (IN THE FORM OF NOE CROSS-PEAKS) WAS COLLECTED FROM 2D NOE EXPERIMENTS IN D2O AS WELL AS IN 90% H2O FOR NON-EXCHANGEABLE AND EXCHANGEABLE PROTONS, RESPECTIVELY. 2D NOE EXPERIMENTS WERE CARRIED OUT AT 50, 80, 200 AND 400 M SEC MIXING TIMES. COUPLING CONSTANTS AND SUGAR CONFORMATIONS WERE DEDUCED FROM DQF-COSY EXPERIMENTS.

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Sample preparation

DetailsContents: D2O AND H2O
Sample conditionsIonic strength: 100 mM NACL / pH: 6.4 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

Software
NameClassification
DYANAmodel building
AMBERrefinement
DYANArefinement
NMR software
NameVersionDeveloperClassification
DYANA1.4GUNTERT,WUTHRICHrefinement
DYANAstructure solution
Amber4.1structure solution
RefinementSoftware ordinal: 1
Details: RANDOMLY GENERATED STRUCTURES WERE FOLDED IN DYANA USING NMR DRIVEN STRUCTURAL RESTRAINTS. 34 STRUCTURES SHOWING LOWEST TARGET FUNCTION VALUES AND NO CONSISTENT VIOLATIONS OF NMR RESTRAINTS ...Details: RANDOMLY GENERATED STRUCTURES WERE FOLDED IN DYANA USING NMR DRIVEN STRUCTURAL RESTRAINTS. 34 STRUCTURES SHOWING LOWEST TARGET FUNCTION VALUES AND NO CONSISTENT VIOLATIONS OF NMR RESTRAINTS WERE INDIVIDUALLY SUBJECTED TO RESTRAINED ENERGY MINIMIZATION IN AMBER 4.1. FOR DETAILS OF REFINEMENT PROTOCOL, PLEASE REFER TO THE REFERENCE ABOVE.
NMR ensembleConformer selection criteria: LOWEST NMR CONSTRAINT VIOLATIONS AND LOWEST AMBER ENERGY.
Conformers calculated total number: 34 / Conformers submitted total number: 1

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