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- PDB-7dd4: Solution structure of an RNA derived from the joint region of the... -

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Basic information

Entry
Database: PDB / ID: 7dd4
TitleSolution structure of an RNA derived from the joint region of the TAR and PolyA stems of HIV-1 genomic RNA
ComponentsRNA (36-MER)
KeywordsRNA / HIV-1 / TAR-PolyA region
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
AuthorsObayashi, C.M. / Shinohara, Y. / Masuda, T. / Kawai, G.
CitationJournal: Sci Rep / Year: 2021
Title: Influence of the 5'-terminal sequences on the 5'-UTR structure of HIV-1 genomic RNA.
Authors: Obayashi, C.M. / Shinohara, Y. / Masuda, T. / Kawai, G.
History
DepositionOct 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: RNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)11,5591
Polymers11,5591
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain RNA (36-MER)


Mass: 11558.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D HOHAHA
151isotropic12D 1H-13C HSQC
131isotropic22D NOESY
141isotropic22D HOHAHA

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Sample preparation

DetailsType: solution
Contents: 100 uM A60-10%13C,15N RNA (36-MER), 95% H2O/5% D2O
Label: A60 / Solvent system: 95% H2O/5% D2O
SampleConc.: 100 uM / Component: RNA (36-MER) / Isotopic labeling: A60-10%13C,15N
Sample conditionsDetails: 20 mM Phosphate buffer (pH 6.5), 50 mM NaCl / Ionic strength: 50 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 11

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