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- PDB-6u79: Solution NMR structure of 5' UTR stem loop B from West Nile Virus -

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Basic information

Entry
Database: PDB / ID: 6u79
TitleSolution NMR structure of 5' UTR stem loop B from West Nile Virus
Components5' UTR region stem loop
KeywordsRNA / Virus / Chemical shift / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesWest Nile virus
MethodSOLUTION NMR / simulated annealing
AuthorsSharma, S. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: NMR structure of Dengue West Nile viruses stem-loop B: A key cis-acting element for flavivirus replication.
Authors: Sharma, S. / Varani, G.
History
DepositionSep 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 2.0Sep 9, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Structure summary
Category: atom_site / citation ...atom_site / citation / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_nmr_ensemble / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_validate_rmsd_angle / struct / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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 / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_nmr_ensemble.conformer_selection_criteria / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.authors / _pdbx_nmr_software.name / _struct.title
Description: Atomic clashes
Details: We are replacing our older atomic coordinates with new atomic coordinates without changing our pdb ID 6U79. Our new atomic coordinates are having better 10 superimposed structures with lower ...Details: We are replacing our older atomic coordinates with new atomic coordinates without changing our pdb ID 6U79. Our new atomic coordinates are having better 10 superimposed structures with lower RMSD and lower atomic clash around 2.
Provider: author / Type: Coordinate replacement
Revision 2.1Sep 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Oct 7, 2020Group: Structure summary / Category: audit_author
Revision 2.3Jan 4, 2023Group: Database references / Other / Structure summary
Category: database_2 / pdbx_SG_project ...database_2 / pdbx_SG_project / pdbx_database_status / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.SG_entry / _struct_keywords.text
Revision 2.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 2.5May 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: 5' UTR region stem loop


Theoretical massNumber of molelcules
Total (without water)11,8411
Polymers11,8411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7180 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 5' UTR region stem loop


Mass: 11841.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) West Nile virus

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic22D NOESY
131isotropic12D 1H-1H TOCSY
141isotropic11H proton
151isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-99% 13C; U-99% 15N] 1, 0.5 mM 99% 13C; U-99% 15N] 2, 0.5 mM [U-99% 13C; U-99% 15N] 3, 0.5 mM [U-99% 13C; U-99% 15N] 4, 0.5 mM [U-99% 13C; U-99% 15N] 5, 90% H2O/10% D2O
Label: WNV_1H / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mM1[U-99% 13C; U-99% 15N]1
0.5 mM299% 13C; U-99% 15N]1
0.5 mM3[U-99% 13C; U-99% 15N]1
0.5 mM4[U-99% 13C; U-99% 15N]1
0.5 mM5[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 20 mM / Label: 1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIBrukerAVANCE II8002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
SparkyGoddardstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 10

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