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- PDB-2m4w: single G-bulge in a conserved regulatory region of the HEV genome -

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Basic information

Entry
Database: PDB / ID: 2m4w
Titlesingle G-bulge in a conserved regulatory region of the HEV genome
ComponentsRNA (5'-R(*GP*GP*AP*AP*UP*CP*GP*AP*AP*AP*GP*AP*UP*GP*UP*CP*C)-3')
KeywordsRNA / G-bulge / internal loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsLescrinier, E.
CitationJournal: To be Published
Title: Binding of a naphtyridine analogue to the single G-bulge in a conserved regulatory region of the HEV genome
Authors: Lescrinier, E.
History
DepositionFeb 11, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 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 (5'-R(*GP*GP*AP*AP*UP*CP*GP*AP*AP*AP*GP*AP*UP*GP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,4901
Polymers5,4901
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)10 / 10all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA (5'-R(*GP*GP*AP*AP*UP*CP*GP*AP*AP*AP*GP*AP*UP*GP*UP*CP*C)-3')


Mass: 5490.349 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC aliphatic
1212D 1H-13C HSQC aromatic
1312D 1H-1H TOCSY
1412D DQF-COSY
1512D 1H-1H NOESY
2622D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM RNA-1, 100% D2O100% D2O
21 mM RNA-2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMRNA-11
1 mMRNA-22
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17ambient 288 K
27278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10 / Representative conformer: 3

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