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- PDB-7ju1: The FARFAR-NMR Ensemble of 29-mer HIV-1 Trans-activation Response... -

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Basic information

Entry
Database: PDB / ID: 7ju1
TitleThe FARFAR-NMR Ensemble of 29-mer HIV-1 Trans-activation Response Element RNA (N=20)
ComponentsRNA (29-MER)
KeywordsRNA / VIRUS RNA / HIV-1 RNA / FARFAR / FARFAR-NMR
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
AuthorsShi, H. / Rangadurai, A. / Roy, R. / Yesselman, J.D. / Al-Hashimi, H.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM132899 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI150470 United States
CitationJournal: Nat Commun / Year: 2020
Title: Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction
Authors: Shi, H. / Rangadurai, A. / Abou-Assi, H. / Roy, R. / Case, D.A. / Herschlag, D. / Yesselman, J.D. / Al-Hashimi, H.M.
History
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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
X: 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: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1lowest energy

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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 1H-13C HSQC
122isotropic12D 1H-13C HSQC
133isotropic12D 1H-13C HSQC
144isotropic12D 1H-13C HSQC
1161isotropic12D 1H-15N HSQC
1152isotropic12D 1H-15N HSQC
1143isotropic12D 1H-15N HSQC
1134isotropic12D 1H-15N HSQC
151anisotropic12D 1H-13C TROSY
182anisotropic12D 1H-13C TROSY
173anisotropic12D 1H-13C TROSY
164anisotropic12D 1H-13C TROSY
1121anisotropic12D 1H-13C S3CT HSQC
1112anisotropic12D 1H-13C S3CT HSQC
1103anisotropic12D 1H-13C S3CT HSQC
194anisotropic12D 1H-13C S3CT HSQC
1201anisotropic12D 1H-15N HSQC without decoupling
1192anisotropic12D 1H-15N HSQC without decoupling
1183anisotropic12D 1H-15N HSQC without decoupling
1174anisotropic12D 1H-15N HSQC without decoupling

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.0 mM 13C,15N mtTAR_E0, 90% H2O/10% D2OUUCGTAR with no elongationmtTAR_E090% H2O/10% D2O
solution21.0 mM 13C,15N mtTAR_EI22, 90% H2O/10% D2OUUCGTAR with Helix I elongated 22 bpsmtTAR_EI2290% H2O/10% D2O
solution31.0 mM 13C,15N mtTAR_EII22, 90% H2O/10% D2OUUCGTAR with Helix II elongated 22 bpsmtTAR_EII2290% H2O/10% D2O
solution41.0 mM 13C,15N mtTAR_EI3, 90% H2O/10% D2OUUCGTAR with Helix I elongated 3 bpsmtTAR_EI390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMmtTAR_E013C,15N1
1.0 mMmtTAR_EI2213C,15N2
1.0 mMmtTAR_EII2213C,15N3
1.0 mMmtTAR_EI313C,15N4
Sample conditionsDetails: 25mM NaCl, 15mM Na3PO4, 0.1mM EDTA / Ionic strength: 25 mM / Label: conditions_1 / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
Details: This is a thermodynamic ensemble in which each confomer is equally populated. The ensemble was generated by sample and select approach which utilize Monte-Carlo simulation annealing.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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