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- PDB-6n8h: RNA Duplex containing the internal loop 5'-GCAU/3'-UACG -

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Basic information

Entry
Database: PDB / ID: 6n8h
TitleRNA Duplex containing the internal loop 5'-GCAU/3'-UACG
ComponentsRNA (5'-R(*CP*GP*GP*GP*CP*AP*UP*CP*CP*G)-3')
KeywordsRNA / Duplex / Internal loop / GU Wobble / CA pair
Function / homologyRNA
Function and homology information
Biological speciesunidentified (others)
MethodSOLUTION NMR / simulated annealing
AuthorsBerger, K.D. / Kennedy, S.D. / Turner, D.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM22939 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM68411-10 United States
CitationJournal: Biochemistry / Year: 2019
Title: Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures.
Authors: Berger, K.D. / Kennedy, S.D. / Turner, D.H.
History
DepositionNov 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,3842
Polymers6,3842
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 3191.964 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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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-13C HSQC
131isotropic1HETCOR

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Sample preparation

DetailsType: solution
Contents: 1 mM RNA (5'-R(*CP*GP*GP*GP*CP*AP*UP*CP*CP*G)-3'), 90% H2O/10% D2O
Label: Natural abundance / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: RNA (5'-R(*CP*GP*GP*GP*CP*AP*UP*CP*CP*G)-3') / Isotopic labeling: none
Sample conditionsIonic strength: 130 Na+ mM / Label: conditions_1 / pH: 6.2 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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