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- PDB-2nc0: Solution structure of the St domain of EMCV IRES -

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Basic information

Entry
Database: PDB / ID: 2nc0
TitleSolution structure of the St domain of EMCV IRES
ComponentsIRES RNA (28-MER)
KeywordsRNA / IRES / translation initiation / Viral RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsImai, S. / D'Souza, V. / Wagner, G.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2016
Title: An accurately preorganized IRES RNA structure enables eIF4G capture for initiation of viral translation.
Authors: Imai, S. / Kumar, P. / Hellen, C.U. / D'Souza, V.M. / Wagner, G.
History
DepositionMar 16, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: pdbx_database_related
Item: _pdbx_database_related.db_id / _pdbx_database_related.db_name
Revision 1.2Jun 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 1.3May 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: IRES RNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)9,1291
Polymers9,1291
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 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain IRES RNA (28-MER)


Mass: 9128.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2222D 1H-1H NOESY
3322D 1H-1H NOESY
1432D 1H-13C HSQC
1533D 1H-13C NOESY
1642D 1H-13C HSQC
1743D 1H-13C NOESY
2852D 1H-15N HSQC
3952D 1H-15N HSQC
21062D 1H-15N HSQC
31162D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM RNA (28-MER), 10 mM potassium phosphate, 10 mM sodium chloride, 100% D2O100% D2O
20.5 mM RNA (28-MER), 10 mM potassium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-13C; U-15N]-Ade, [U-13C; U-15N]-Cyt RNA (28-MER), 10 mM potassium phosphate, 10 mM sodium chloride, 100% D2O100% D2O
40.5 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura RNA (28-MER), 10 mM potassium phosphate, 10 mM sodium chloride, 100% D2O100% D2O
50.5 mM [U-13C; U-15N]-Ade, [U-13C; U-15N]-Cyt RNA (28-MER), 10 mM potassium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
60.5 mM [U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura RNA (28-MER), 10 mM potassium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMRNA (28-MER)-11
10 mMpotassium phosphate-21
10 mMsodium chloride-31
0.5 mMRNA (28-MER)-42
10 mMpotassium phosphate-52
10 mMsodium chloride-62
0.5 mMRNA (28-MER)-7[U-13C; U-15N]-Ade, [U-13C; U-15N]-Cyt3
10 mMpotassium phosphate-83
10 mMsodium chloride-93
0.5 mMRNA (28-MER)-10[U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura4
10 mMpotassium phosphate-114
10 mMsodium chloride-124
0.5 mMRNA (28-MER)-13[U-13C; U-15N]-Ade, [U-13C; U-15N]-Cyt5
10 mMpotassium phosphate-145
10 mMsodium chloride-155
0.5 mMRNA (28-MER)-16[U-13C; U-15N]-Gua, [U-13C; U-15N]-Ura6
10 mMpotassium phosphate-176
10 mMsodium chloride-186
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1206.5ambient 308 K
2206.5ambient 283 K
3205.5ambient 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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