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- PDB-8thv: FARFAR-NMR ensemble of HIV-1 TAR with apical loop capturing groun... -

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Basic information

Entry
Database: PDB / ID: 8thv
TitleFARFAR-NMR ensemble of HIV-1 TAR with apical loop capturing ground and excited conformational states
ComponentsRNA (29-MER)
KeywordsRNA / Viral RNA / HIV-1 TAR / Excited Conformational States
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
AuthorsRoy, R. / Geng, A. / Shi, H. / Merriman, D.K. / Dethoff, E.A. / Salmon, L. / Al-Hashimi, H.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM132899 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 AI150470 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble.
Authors: Roy, R. / Geng, A. / Shi, H. / Merriman, D.K. / Dethoff, E.A. / Salmon, L. / Al-Hashimi, H.M.
History
DepositionJul 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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Assembly

Deposited unit
A: RNA (29-MER)


Theoretical massNumber of molelcules
Total (without water)9,3081
Polymers9,3081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1target function

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Components

#1: RNA chain RNA (29-MER)


Mass: 9307.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 13C-1H S3CT HSQC
121anisotropic12D 13C-1H S3CT HSQC
132isotropic22D 13C-1H S3CT HSQC
142anisotropic22D 13C-1H S3CT HSQC
153isotropic32D 13C-1H S3CT HSQC
163anisotropic32D 13C-1H S3CT HSQC
1174isotropic12D 13C-1H S3CT HSQC
1164anisotropic12D 13C-1H S3CT HSQC
1151isotropic12D 13C-1H TROSY HSQC
1141anisotropic12D 13C-1H TROSY HSQC
1132isotropic22D 13C-1H TROSY HSQC
1122anisotropic22D 13C-1H TROSY HSQC
1113isotropic32D 13C-1H TROSY HSQC
1103anisotropic32D 13C-1H TROSY HSQC
194isotropic12D 13C-1H TROSY HSQC
184anisotropic12D 13C-1H TROSY HSQC
1181isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM 13C, 15N E0_wt_TAR RNA (29-MER), 90% H2O/10% D2OE0_wt_TAR90% H2O/10% D2O
solution21.0 mM 13C, 15N EI22_wt_TAR RNA (29-MER), 90% H2O/10% D2OEI22_wt_TAR90% H2O/10% D2O
solution31.0 mM 13C, 15N EII3_wt_TAR RNA (29-MER), 90% H2O/10% D2OEII3_wt_TAR90% H2O/10% D2O
solution41.0 mM 13C, 15N EII13_wt_TAR RNA (29-MER), 90% H2O/10% D2OEII13_wt_TAR90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mME0_wt_TAR RNA (29-MER)13C, 15N1
1.0 mMEI22_wt_TAR RNA (29-MER)13C, 15N2
1.0 mMEII3_wt_TAR RNA (29-MER)13C, 15N3
1.0 mMEII13_wt_TAR RNA (29-MER)13C, 15N4
Sample conditionsDetails: 15 mM Na3PO4, 25 mM NaCl, 0.1 mM EDTA, 10% D2O / Ionic strength: 25 mM / Label: wt-TAR in NMR buffer / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001HCN cryoprobe
Agilent VarianAgilentVarian8002HCN cryoprobe
Agilent VarianAgilentVarian6003HCN cryoprobe

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RosettaShi et alstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2 / Details: FARFAR-NMR
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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