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- PDB-1rfr: NMR structure of the 30mer stemloop-D of coxsackieviral RNA -

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Basic information

Entry
Database: PDB / ID: 1rfr
TitleNMR structure of the 30mer stemloop-D of coxsackieviral RNA
Componentsstemloop-D RNA of the 5'-cloverleaf of coxsackievirus B3
KeywordsRNA / loop with conformation similar to stable UNCG-tetraloops and U:G closing base pair / base-paired U:U-C:U-U:U mismatch / A-form helix stems
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHuman coxsackievirus B3
MethodSOLUTION NMR / distance geometry, simulated annealing, energy minimisation
AuthorsOhlenschlager, O. / Wohnert, J. / Bucci, E. / Seitz, S. / Hafner, S. / Ramachandran, R. / Zell, R. / Gorlach, M.
CitationJournal: STRUCTURE / Year: 2004
Title: The structure of the stemloop D subdomain of coxsackievirus B3 cloverleaf RNA and its interaction with the proteinase 3C.
Authors: Ohlenschlager, O. / Wohnert, J. / Bucci, E. / Seitz, S. / Hafner, S. / Ramachandran, R. / Zell, R. / Gorlach, M.
History
DepositionNov 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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: stemloop-D RNA of the 5'-cloverleaf of coxsackievirus B3


Theoretical massNumber of molelcules
Total (without water)9,5371
Polymers9,5371
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)20 / 100structures with the lowest energy,target function
RepresentativeModel #1closest to the average

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Components

#1: RNA chain stemloop-D RNA of the 5'-cloverleaf of coxsackievirus B3


Mass: 9536.624 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PROTEINASE 3C BINDING DOMAIN / Source: (gene. exp.) Human coxsackievirus B3 / Genus: Enterovirus / Species: Human enterovirus B
Description: two nucleotides (GG) at 5'-end and two nucleotides (UC) at the 3'-end were added for in vitro production
Gene: 5'-nontranslated region / Plasmid: pUC-19 / Production host: in vitro (unknown)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: see below
NMR detailsText: the structure was determined using heteronuclear 2D and 3D NMR experiments, e.g. 3D HCCH-COSY, RELAY-COSY, TOCSY, H6/H5(C4N)H, C6/C5(C4N)H, H(CCN)H-TOCSY, HCCH-TOCSY, 2D H(N)CO, 2D CPMG-HSQC- ...Text: the structure was determined using heteronuclear 2D and 3D NMR experiments, e.g. 3D HCCH-COSY, RELAY-COSY, TOCSY, H6/H5(C4N)H, C6/C5(C4N)H, H(CCN)H-TOCSY, HCCH-TOCSY, 2D H(N)CO, 2D CPMG-HSQC-NOESY, 2D NOESY, 3D 1H,1H,15N-NOESY-HSQC, 3D 1H,1H,13C-NOESY-HSQC, CLEAN-TOCSY, 31P-SPINECHO-DIFFERENCE-CT-HMQC, HNN-COSY, 2D 1H,13C-HSQC, 2D 1H,15N-HSQC, HCN, H5(C5C4N)H, H8(C8C2)H2, 3D 13C-F1-FILTERED,13C-F3-EDITED-NOESY-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9mM SLD-RNA U-15N,13C; 10mM KH2PO4/K2HPO4, 40mM KCl, 0.2mM EDTA95% H2O, 5% v/v D2O or 99.99% v/v D2O
21.2mM SLD-RNA G,C-15N,13C; 10mM KH2PO4/K2HPO4, 40mM KCl, 0.2mM EDTA95% H2O, 5% v/v D2O or 99.99% v/v D2O
31.2mM SLD-RNA A,U-15N,13C; 10mM KH2PO4/K2HPO4, 40mM KCl, 0.2mM EDTA95% H2O, 5% v/v D2O or 99.99% v/v D2O
41.4mM SLD-RNA U-15N; 10mM KH2PO4/K2HPO4, 40mM KCl, 0.2mM EDTA95% H2O, 5% v/v D2O or 99.99% v/v D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM KH2PO4/K2HPO4, 40mM KCl, 0.2mM EDTA 6.2 ambient 298 K
210mM KH2PO4/K2HPO4, 40mM KCl, 0.2mM EDTA 6.2 ambient 283 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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1, rev. cVarian Inc.collection
VNMR6.1, rev. cVarian Inc.processing
XEASY1.3.9Bartelsdata analysis
FOUNDimplemented in CYANA-1.0.6Guntertstructure solution
CYANA1.0.6Herrmannstructure solution
OPAL2.6Luginbuhlrefinement
RefinementMethod: distance geometry, simulated annealing, energy minimisation
Software ordinal: 1
Details: 1001 experimental distances derived from NOE cross peaks, 280 torsion angle constraints describing 258 torsion angles, 52 hydrogen bond constraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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