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- PDB-1r7w: NMR STRUCTURE OF THE R(GGAGGACAUCCCUCACGGGUGACCGUGGUCCUCC), DOMAI... -

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Basic information

Entry
Database: PDB / ID: 1r7w
TitleNMR STRUCTURE OF THE R(GGAGGACAUCCCUCACGGGUGACCGUGGUCCUCC), DOMAIN IV STEM-LOOP B OF ENTEROVIRAL IRES WITH AUCCCU BULGE
Components34-MER
KeywordsRNA / STEM-AND-LOOP STRUCTURE / SIX-NUCLEOTIDE BULGE / GUGA TETRALOOP
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / FULL MATRIX RELAXATION ANALYSIS OF NOE, RANDOM ERROR ANALYSIS OF NOE, SIMULATED ANNEALING USING RESTRAINED MOLECULAR DYNAMICS
AuthorsDu, Z. / Ulyanov, N.B. / Yu, J. / James, T.L.
CitationJournal: Biochemistry / Year: 2004
Title: NMR Structures of Loop B RNAs from the Stem-Loop IV Domain of the Enterovirus Internal Ribosome Entry Site: A Single C to U Substitution Drastically Changes the Shape and Flexibility of RNA(,).
Authors: Du, Z. / Ulyanov, N.B. / Yu, J. / Andino, R. / James, T.L.
History
DepositionOct 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 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: 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: 34-MER


Theoretical massNumber of molelcules
Total (without water)10,8981
Polymers10,8981
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)20 / 50LOWEST TOTAL ENERGY (A WEIGHTED SUM OF CONFORMATIONAL ENERGY AND RESTRAINT ENERGY)
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 34-MER


Mass: 10897.511 Da / Num. of mol.: 1 / Fragment: DOMAIN IV, LOOP B / Mutation: SEQUENCE VARIANT WITH THE AUCCCU BULGE / Source method: obtained synthetically
Details: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
232DQF-COSY
2433D 13C-separated NOESY
2571H-13C CONSTANT TIME HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM unlabeled RNA, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), 90% H2O, 10% D2O90% H2O/10% D2O
21mM unlabeled RNA, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), D2OD2O
31mM of uniformly labeled RNA with 13C, 15N, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), 90% H2O, 10% D2O90% H2O/10% D2O
41mM of uniformly labeled RNA with 13C, 15N, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), D2OD2O
51mM of RNA labeled in residues A and U with 13C, 15N, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), D2OD2O
61mM of RNA labeled in residues C with 13C, 15N, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), D2OD2O
71mM of uniformly labeled RNA with 13C, 15N, 25mM NaCl, 25mM sodium phosphate buffer (pH 6.5), 5% (weight/volume) of C12E6/n-hexanol mixture (molar ratio 0.64), D2OD2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM Na+ ions 6.5 ambient 283 K
250 mM Na+ ions 6.5 ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Associates, Inc.collection
NMRPipe2.1F.Delaglioprocessing
MARDIGRAS3.2T.L.Jamesiterative matrix relaxation
DYANA1.5P.Guntertrefinement
Amber7D.A.Caserefinement
RefinementMethod: FULL MATRIX RELAXATION ANALYSIS OF NOE, RANDOM ERROR ANALYSIS OF NOE, SIMULATED ANNEALING USING RESTRAINED MOLECULAR DYNAMICS
Software ordinal: 1
Details: STRUCTURES ARE REFINED BASED ON 575 NOE-DERIVED DISTANCES AND 86 RESIDUAL DIPOLAR COUPLINGS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: LOWEST TOTAL ENERGY (A WEIGHTED SUM OF CONFORMATIONAL ENERGY AND RESTRAINT ENERGY)
Conformers calculated total number: 50 / Conformers submitted total number: 20

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