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- PDB-8k8b: Solution structure of a hairpin RNA with the UUCGA loop -

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Entry
Database: PDB / ID: 8k8b
TitleSolution structure of a hairpin RNA with the UUCGA loop
ComponentsRNA (5'-R(*GP*GP*AP*UP*CP*CP*UP*UP*UP*CP*GP*AP*GP*GP*GP*AP*UP*CP*C)-3')
KeywordsRNA / penta loop / UUCG loop
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsIchijo, R. / Kawai, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem Biophys Res Commun / Year: 2024
Title: NMR analysis of a loop-bulge structure of UUCGA pentaloop.
Authors: Rika Ichijo / Gota Kawai /
Abstract: Although structures of many RNA loops, such as GNRA and UNCG tetraloops, were well known, it is still possible to find more RNA structures. In the present study, solution structure of an RNA fragment ...Although structures of many RNA loops, such as GNRA and UNCG tetraloops, were well known, it is still possible to find more RNA structures. In the present study, solution structure of an RNA fragment having UUCGA pentaloop was analyzed by NMR spectroscopy. It was found that the UUCG tetraloop is formed and the adenosine residue at the 3' side of the tetraloop is bulged out. The characteristic motif of the loop-bulge structure has also been found in other RNAs including CUUGU and CUGGC pentaloops. Along with the recently found T-hairpin structure with a UUUGAUU loop, in which UUUGA pentaloop and UU bulge are formed, the loop-bulge structures can be categorized as an RNA motif and it may be called as the integrated structure loop, I-loop.
History
DepositionJul 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*AP*UP*CP*CP*UP*UP*UP*CP*GP*AP*GP*GP*GP*AP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,0711
Polymers6,0711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 (5'-R(*GP*GP*AP*UP*CP*CP*UP*UP*UP*CP*GP*AP*GP*GP*GP*AP*UP*CP*C)-3')


Mass: 6070.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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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

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Sample preparation

DetailsType: solution
Contents: 0.36 mM RNA (5'-R(*GP*GP*AP*UP*CP*CP*UP*UP*UP*CP*GP*AP*GP*GP*GP*AP*UP*CP*C)-3'), 95% H2O/5% D2O
Label: Sample1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.36 mM
Component: RNA (5'-R(*GP*GP*AP*UP*CP*CP*UP*UP*UP*CP*GP*AP*GP*GP*GP*AP*UP*CP*C)-3')
Isotopic labeling: none
Sample conditionsIonic strength: 50 mM / Label: condition1 / 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
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
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: 100 / Conformers submitted total number: 11

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