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- PDB-1m82: SOLUTION STRUCTURE OF THE COMPLEMENTARY RNA PROMOTER OF INFLUENZA... -

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Basic information

Entry
Database: PDB / ID: 1m82
TitleSOLUTION STRUCTURE OF THE COMPLEMENTARY RNA PROMOTER OF INFLUENZA A VIRUS
ComponentsRNA (25-MER): THE COMPLEMENTARY RNA PROMOTER OF INFLUENZA A VIRUS
KeywordsRNA / asymmetric internal loop / A-form helix
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPark, C.-J. / Bae, S.-H. / Lee, M.-K. / Varani, G. / Choi, B.-S.
CitationJournal: NUCLEIC ACIDS RES. / Year: 2003
Title: Solution structure of the influenza A virus cRNA promoter: implications for differential recognition of viral promoter structures by RNA-dependent RNA polymerase
Authors: Park, C.-J. / Bae, S.-H. / Lee, M.-K. / Varani, G. / Choi, B.-S.
History
DepositionJul 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: 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: 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
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: RNA (25-MER): THE COMPLEMENTARY RNA PROMOTER OF INFLUENZA A VIRUS


Theoretical massNumber of molelcules
Total (without water)7,9841
Polymers7,9841
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)31 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #21lowest energy

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Components

#1: RNA chain RNA (25-MER): THE COMPLEMENTARY RNA PROMOTER OF INFLUENZA A VIRUS


Mass: 7983.740 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in complementary RNA of the influenza A virus genome segments.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D NOESY
2212D NOESY
2312D TOCSY
241DQF-COSY
2532D NOESY
2642D NOESY
271HETCOR
2813D 13C NOESY-HSQC
2913D (H)CCH-COSY
21013D (H)CCH-COSY-TOCSY
NMR detailsText: The structure was determined using 3D heteronuclear nmr spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM influenza A virus cRNA promoter (25mer) 20mM phosphate buffer(pH 6.0)0.1mM EDTA90% H2O/10% D2O
21mM influenza A virus cRNA promoter (25mer) U-15N, 13C; 20mM phosphate buffer(pH 6.0)0.1mM EDTA100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM NaPi 0.1mM EDTA 6.0 ambient 300 K
220mM NaPi 0.1mM EDTA 6.0 ambient 280 K
320mM NaPi 0.1mM EDTA 6.0 ambient 290 K
420mM NaPi 0.1mM EDTA 6.0 ambient 310 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 DMXBrukerDMX6001
Bruker DMXBrukerDMX8002
Bruker AMXBrukerAMX5003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
Felix95Biosym,inc.processing
VNMR6.1cVarian, inc.collection
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 834 restraints, 592 are NOE-derived distance restraints, 140 torsion angle restraints, 54 planarity restraints and 48 base-pair restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 31

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