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- PDB-7ume: DENV1 SLA top stemloop RNA (DenvTSL) -

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Basic information

Entry
Database: PDB / ID: 7ume
TitleDENV1 SLA top stemloop RNA (DenvTSL)
ComponentsRNA (28-MER)
KeywordsRNA / flavivirus / 5' UTR / SLA / viral replication / NS5 promoter / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesDengue virus 1
MethodSOLUTION NMR / simulated annealing
AuthorsSun, Y.T. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Rna / Year: 2022
Title: Structure of the dengue virus RNA promoter.
Authors: Sun, Y.T. / Varani, G.
History
DepositionApr 6, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionJul 6, 2022ID: 7LM1
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Aug 24, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 4, 2023Group: Other / Structure summary
Category: pdbx_SG_project / pdbx_database_status / struct_keywords
Item: _pdbx_database_status.SG_entry / _struct_keywords.text
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5May 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)9,0161
Polymers9,0161
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (28-MER)


Mass: 9016.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Dengue 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 1H-1H TOCSY
122isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
142isotropic12D 1H-1H NOESY
153isotropic12D 1H-1H NOESY
164isotropic12D 1H-13C HSQC
174isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM RNA (28-MER), 10 mM potassium phosphate, 95% H2O/5% D2O1H_h2o95% H2O/5% D2O
solution21 mM RNA (28-MER), 10 mM potassium phosphate, 100% D2O1H_d2o100% D2O
solution31 mM [U-2H] RNA (28-MER), 10 mM potassium phosphate, 100% D2O2D_d2o100% D2O
solution41 mM [U-100% 13C; U-100% 15N] RNA (28-MER), 10 mM potassium phosphate, 100% D2ONC_h2o100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRNA (28-MER)natural abundance1
10 mMpotassium phosphatenatural abundance1
1 mMRNA (28-MER)natural abundance2
10 mMpotassium phosphatenatural abundance2
1 mMRNA (28-MER)[U-2H]3
10 mMpotassium phosphatenatural abundance3
1 mMRNA (28-MER)[U-100% 13C; U-100% 15N]4
10 mMpotassium phosphatenatural abundance4
Sample conditionsIonic strength: 50 mM / Label: condition1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRFAM-SPARKYNMRFAM-SPARKYpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRFAM-SPARKYNMRFAM-SPARKYchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 10

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