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- PDB-2ljj: The structure of subdomain IV-B from the CVB-3 IRES -

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Basic information

Entry
Database: PDB / ID: 2ljj
TitleThe structure of subdomain IV-B from the CVB-3 IRES
ComponentsIV-B RNA
KeywordsRNA / hairpin / Coxsackievirus B3 / Internal Ribosomal Entry Site
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing
Model detailsfewest violations, model 1
AuthorsIhle, Y. / Zell, R. / Goerlach, M.
CitationJournal: To be Published
Title: The Structure of Subdomain IV-B from the CVB-3 IRES
Authors: Ihle, Y.
History
DepositionSep 15, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: 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: IV-B RNA


Theoretical massNumber of molelcules
Total (without water)8,6001
Polymers8,6001
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 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: RNA chain IV-B RNA


Mass: 8600.159 Da / Num. of mol.: 1 / Fragment: subdomain IV-B / Source method: obtained synthetically / Details: in vitro transcription, T7 RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H15N-NOESY-HSQC
1212D TOCSY
2312D HNN-COSY
1412D 1H1H-NOESY WATERGATE
2512D 1H1H-NOESY WATERGATE
1612D 1H-1H NOESY
1712D 15N-HSQC imino
2812D 15N-HSQC imino
1912D 15N-HSQC amino
21012D 15N-HSQC amino
21123D (H)CCH-TOCSY
21223D (H)CCH-COSY
21323D 1H13C-NOESY-HSQC aro
21423D 1H13C-NOESY-HSQC ali
21522D HcN ali
21622D HcN aro
21722D (H)CCH-TOCSY ADE
21822D H5(c5c4n)H ura
11922D H5(c5c4n)H cyt
22022D 13C-HSQC-CT ali
22122D 13C-HSQC-CT aro
22221D 31P
22333D (H)CCH-TOCSY
22433D (H)CCH-COSY
22533D 1H1H13C-NOESY-HSQC 13C-filtered
22633D 1H13C-NOESY-HSQC aro
22733D 1H13C-NOESY-HSQC ali
22832D 13C-HSQC ali
22932D 13C-HSQC aro
23043D (H)CCH-TOCSY
23143D (H)CCH-COSY
23243D 1H1H13C-NOESY-HSQC 13C-filtered
23343D 1H13C-NOESY-HSQC aro
23443D 1H13C-NOESY-HSQC ali
23542D TOCSY(HSQC)
23642D HcN ali
23742D 1H-1H NOESY
13842D 13C-HSQC ali
23942D 13C-HSQC ali
14042D 13C-HSQC aro
24142D 13C-HSQC aro

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] IV-B RNA, 10 mM potassium phosphate, 40 mM potassium chloride, 200 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] IV-B RNA, 10 mM potassium phosphate, 40 mM potassium chloride, 200 uM EDTA, 100% D2O100% D2O
31 mM [U-13C; U-15N]-Gua,Ura IV-B RNA, 10 mM potassium phosphate, 40 mM potassium chloride, 200 uM EDTA, 100% D2O100% D2O
41 mM [U-13C; U-15N]-Ade,Cyt IV-B RNA, 10 mM potassium phosphate, 40 mM potassium chloride, 200 uM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMIV-B RNA-1[U-100% 15N]1
10 mMpotassium phosphate-21
40 mMpotassium chloride-31
200 uMEDTA-41
1 mMIV-B RNA-5[U-100% 13C; U-100% 15N]2
10 mMpotassium phosphate-62
40 mMpotassium chloride-72
200 uMEDTA-82
1 mMIV-B RNA-9[U-13C; U-15N]-Ade,Cyt3
10 mMpotassium phosphate-103
40 mMpotassium chloride-113
200 uMEDTA-123
1 mMIV-B RNA-13[U-13C; U-15N]-Gua,Ura4
10 mMpotassium phosphate-144
40 mMpotassium chloride-154
200 uMEDTA-164
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 6.2 ambient 283 K
250 6.2 ambient 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.1Guntert, Mumenthaler and Wuthrichstructure solution
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.5.5Rochus Kellerchemical shift assignment
CARA1.5.5Rochus Kellerpeak picking
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA1.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR constraintsNA alpha-angle constraints total count: 26 / NA beta-angle constraints total count: 26 / NA chi-angle constraints total count: 27 / NA delta-angle constraints total count: 27 / NA epsilon-angle constraints total count: 26 / NA gamma-angle constraints total count: 27 / NA other-angle constraints total count: 79 / NA sugar pucker constraints total count: 19 / NOE constraints total: 792 / NOE intraresidue total count: 364 / NOE long range total count: 82 / NOE medium range total count: 14 / NOE sequential total count: 332 / Hydrogen bond constraints total count: 76
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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