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- PDB-8jhp: Another hairpin structure found in the RNA element involved in pi... -

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Basic information

Entry
Database: PDB / ID: 8jhp
TitleAnother hairpin structure found in the RNA element involved in piRNA biogenesis
ComponentsRNA (27-MER)
KeywordsRNA / cis element
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsTakase, N. / Kawai, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Another hairpin structure found in the RNA element involved in piRNA biogenesis
Authors: Takase, N. / Kawai, G.
History
DepositionMay 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)8,6421
Polymers8,6421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain RNA (27-MER)


Mass: 8642.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H HOHAHA

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Sample preparation

DetailsType: solution / Contents: 0.13 mM RNA (27-MER), 95% H2O/5% D2O / Label: sample_1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.13 mM / Component: RNA (27-MER) / Isotopic labeling: none
Sample conditionsIonic strength: 50 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.114Goddardchemical shift assignment
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Sparky3.114Goddardpeak 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: 100 / Conformers submitted total number: 11

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