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- PDB-6xb7: IRES-targeting Small Molecule Inhibits Enterovirus 71 Replication... -

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Basic information

Entry
Database: PDB / ID: 6xb7
TitleIRES-targeting Small Molecule Inhibits Enterovirus 71 Replication via Allosteric Stabilization of a Ternary Complex
ComponentsRNA (41-MER)
KeywordsRNA / RNA-small molecule complex / RNA binding protein
Function / homologyChem-UYS / RNA / RNA (> 10)
Function and homology information
Biological speciesEnterovirus A71
MethodSOLUTION NMR / molecular dynamics
AuthorsTolbert, B.S. / Davila, J. / Sugarman, A.L. / Chiu, L.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM126833 United States
CitationJournal: Nat Commun / Year: 2020
Title: IRES-targeting small molecule inhibits enterovirus 71 replication via allosteric stabilization of a ternary complex.
Authors: Davila-Calderon, J. / Patwardhan, N.N. / Chiu, L.Y. / Sugarman, A. / Cai, Z. / Penutmutchu, S.R. / Li, M.L. / Brewer, G. / Hargrove, A.E. / Tolbert, B.S.
History
DepositionJun 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4642
Polymers13,1411
Non-polymers3231
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 16structures 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
#2: Chemical ChemComp-UYS / 3-amino-N-(diaminomethylidene)-5-(dimethylamino)-6-(phenylethynyl)pyrazine-2-carboxamide


Mass: 323.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N7O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-1H NOESY
122isotropic32D 1H-1H NOESY
133isotropic32D 1H-1H NOESY
144isotropic32D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1200 uM Selective Deuteration; Fully Deuteration for U and C; Selective Deuteration for A and G rNTP, 800 uM DMA135, 100% D2OSL2: DMA135=1:4 molar ratioSL2_DMA135_complex_AG_selective_labeling100% D2O
solution2200 uM Selective Deuteration; EQUIMOLAR MIX:ATP, GTP, CTP, UTP rNTP, 800 uM DMA135, 100% D2OSL2_DMA135_complex_EqualMolar_labeling100% D2O
solution3200 uM Selective Deuteration; Fully Deuteration for U and C; Selective Deuteration for A and G rNTP, 100% D2OSL2 onlySL2_free_AG_selective_labeling100% D2O
solution4200 uM Selective Deuteration; EQUIMOLAR MIX:ATP, GTP, CTP, UTP rNTP, 100% D2OSL2_free_EqualMolar_labeling100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMrNTPSelective Deuteration; Fully Deuteration for U and C; Selective Deuteration for A and G1
800 uMDMA135natural abundance1
200 uMrNTPSelective Deuteration; EQUIMOLAR MIX:ATP, GTP, CTP, UTP2
200 uMrNTPSelective Deuteration; Fully Deuteration for U and C; Selective Deuteration for A and G3
200 uMrNTPSelective Deuteration; EQUIMOLAR MIX:ATP, GTP, CTP, UTP4
800 uMDMA135natural abundance2
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
NMRViewJohnson, One Moon Scientificchemical shift assignment
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 16 / Conformers submitted total number: 10

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