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- PDB-1mfy: SOLUTION STRUCTURE OF INFLUENZA A VIRUS C4 PROMOTER -

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Basic information

Entry
Database: PDB / ID: 1mfy
TitleSOLUTION STRUCTURE OF INFLUENZA A VIRUS C4 PROMOTER
ComponentsC4 promoter of influneza A virus
KeywordsRNA / Influenza A virus promoter / internal loop / single adenine bulge / C4 / natural variant
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing
Model type detailsminimized average
AuthorsLee, M.-K. / Bae, S.-H. / Park, C.-J. / Cheong, H.-K. / Cheong, C. / Choi, B.-S.
CitationJournal: Nucleic Acids Res. / Year: 2003
Title: A single-nucleotide natural variation (U4 to C4) in an influenza A virus promoter exhibits a large structural change: implications for differential viral RNA synthesis by RNA-dependent RNA polymerase.
Authors: Lee, M.-K. / Bae, S.-H. / Park, C.-J. / Cheong, H.-K. / Cheong, C. / Choi, B.-S.
History
DepositionAug 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C4 promoter of influneza A virus


Theoretical massNumber of molelcules
Total (without water)9,9121
Polymers9,9121
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain C4 promoter of influneza A virus


Mass: 9911.909 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in influenza A virus.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
122DQF-COSY
1322D NOESY
1443D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1Unlabeled RNA, 1mM90% H2O/10% D2O
2Unlabeled RNA, 1mM99.96% D2O,
3Uniform labeling with 13C,15N90% H2O/10% D2O
4Uniform labeling with 13C,15N99.96% D2O,
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
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger et alstructure solution
NMRPipe2.1Delaglio et alprocessing
CNS1Brunger et alrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 726 restraints, 445 are NOE-derived distance constraints, 196 dihedral angle restraints, 58 hydrogen bonding restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 16

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