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- PDB-1jo7: Solution Structure of Influenza A Virus Promoter -

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Basic information

Entry
Database: PDB / ID: 1jo7
TitleSolution Structure of Influenza A Virus Promoter
ComponentsInfluenza A virus promoter RNA
KeywordsRNA / RNA panhandle / AAU AC mismatch / bending / internal loop / UUCG
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / Distance geometry, Simulated annealing + Susceptibility anisotropy
AuthorsBae, S.-H. / Cheong, H.-K. / Lee, J.-H. / Cheong, C. / Kainosho, M. / Choi, B.-S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structural features of an influenza virus promoter and their implications for viral RNA synthesis.
Authors: Bae, S.H. / Cheong, H.K. / Lee, J.H. / Cheong, C. / Kainosho, M. / Choi, B.S.
History
DepositionJul 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Influenza A virus promoter RNA


Theoretical massNumber of molelcules
Total (without water)9,9131
Polymers9,9131
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 200The submitted conformer models are the 32 structures with lowest energy and acceptable covalent geometry
RepresentativeModel #1major conformers(1-15)

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Components

#1: RNA chain Influenza A virus promoter RNA


Mass: 9912.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 in vitro transcription

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: DQF-COSY
NMR detailsText: The structure was determined using standard 2D and 3D techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM unlabeled90%H2O/10%D2O or 99.996% D2O
20.4mM 13C/15N labeled90%H2O/10%D2O or 99.996% D2O
30.4mM 13C/15N labeled90%H2O/10%D2O + PM (purple membrane)
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM sodium phosphate 6.5 ambient 294 K
210mM sodium phosphate 6.5 ambient 277 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX4003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR98Bruker Inc.processing
Sparky3.95UCSFdata analysis
X-PLOR3.1Brunger et al.refinement
CNS1Brunger et al.refinement
RefinementMethod: Distance geometry, Simulated annealing + Susceptibility anisotropy
Software ordinal: 1
Details: The structures are refined using residual dipolar coupling constraints
NMR representativeSelection criteria: major conformers(1-15)
NMR ensembleConformer selection criteria: The submitted conformer models are the 32 structures with lowest energy and acceptable covalent geometry
Conformers calculated total number: 200 / Conformers submitted total number: 32

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