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- PDB-5v16: HnRNP A1 Alters the Conformation of a Conserved Enterovirus IRES ... -

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Basic information

Entry
Database: PDB / ID: 5v16
TitleHnRNP A1 Alters the Conformation of a Conserved Enterovirus IRES Domain to Stimulate Viral Translation
ComponentsRNA (41-MER)
KeywordsRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEnterovirus A71
MethodSOLUTION NMR / molecular dynamics
AuthorsTolbert, M. / Morgan, C.E. / Tolbert, B.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM101979 United States
CitationJournal: J. Mol. Biol. / Year: 2017
Title: HnRNP A1 Alters the Structure of a Conserved Enterovirus IRES Domain to Stimulate Viral Translation.
Authors: Tolbert, M. / Morgan, C.E. / Pollum, M. / Crespo-Hernandez, C.E. / Li, M.L. / Brewer, G. / Tolbert, B.S.
History
DepositionMar 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (41-MER)


Theoretical massNumber of molelcules
Total (without water)13,1411
Polymers13,1411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1024structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (41-MER)


Mass: 13140.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterovirus A71

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-1H NOESY
124isotropic22D 1H-13C HMQC
132isotropic22D 1H-1H TOCSY
143isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1180.0 uM Selective Deuteration; EQUIMOLAR MIX:ATP, GTP, CTP, UTP rNTP, 100% D2OSL2 WT, 100% D2O100% D2O
solution2300.0 uM Fully protonated rNTP, 100% D2OSL2 WT, TOCSY100% D2O
solution3100.0 uM Fully protonated rNTP, 100% D2OSL2 WT, 100% D2O100% D2O
solution4300.0 uM [U-13C]-Gua rNTP, 100% D2OSL2 WT, HMQC100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
180.0 uMrNTPSelective Deuteration; EQUIMOLAR MIX:ATP, GTP, CTP, UTP1
300.0 uMrNTPFully protonated2
100.0 uMrNTPFully protonated3
300.0 uMrNTP[U-13C]-Gua4
Sample conditionsIonic strength: 10 mM / Label: SL2 WT / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1024 / Conformers submitted total number: 10

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