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- PDB-7lva: Solution structure of the HIV-1 PBS-segment -

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Basic information

Entry
Database: PDB / ID: 7lva
TitleSolution structure of the HIV-1 PBS-segment
ComponentsRNA (103-MER)
KeywordsRNA / Primer binding site / reverse transcription
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / SOLUTION SCATTERING / molecular dynamics / distance geometry
AuthorsHeng, X. / Song, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI150460 United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity.
Authors: Song, Z. / Gremminger, T. / Singh, G. / Cheng, Y. / Li, J. / Qiu, L. / Ji, J. / Lange, M.J. / Zuo, X. / Chen, S.J. / Zou, X. / Boris-Lawrie, K. / Heng, X.
History
DepositionFeb 24, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionMar 17, 2021ID: 7K1Z
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 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 1.4May 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: RNA (103-MER)


Theoretical massNumber of molelcules
Total (without water)33,2501
Polymers33,2501
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 / 1200target function
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (103-MER)


Mass: 33249.836 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

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
122isotropic12D 1H-1H NOESY
133isotropic12D 1H-1H NOESY
144isotropic12D 1H-1H NOESY
155isotropic12D 1H-1H NOESY
166isotropic12D 1H-1H NOESY
177isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1250 uM 1H RNA (103-MER), 100% D2O1H_sample100% D2O
solution2250 uM A-8D, C-D, G-H, U-5,6-D2 RNA (103-MER), 100% D2OA-8D, C-D, G-H, U-5,6-D2100% D2O
solution3250 uM A-8D, C-D, G-8D, U-H RNA (103-MER), 100% D2OA-8D, C-D, G-8D, U-H100% D2O
solution4250 uM A-8D, C-5,6-D2, G-D, U-5,6-D2 RNA (103-MER), 100% D2OA-8D, C-5,6-D2, G-D, U-5,6-D2100% D2O
solution5250 uM A-8D, C-D, G-8D, U-D RNA (103-MER), 100% D2OA-8D, C-D, G-8D, U-D100% D2O
solution6250 uM A-H, C-D, G-H, U-D RNA (103-MER), 100% D2OA-H, C-D, G-H, U-D100% D2O
solution7250 uM A-H, C-H, G-D, U-D RNA (103-MER), 100% D2OA-H, C-H, G-D, U-D100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
250 uMRNA (103-MER)1H1
250 uMRNA (103-MER)A-8D, C-D, G-H, U-5,6-D22
250 uMRNA (103-MER)A-8D, C-D, G-8D, U-H3
250 uMRNA (103-MER)A-8D, C-5,6-D2, G-D, U-5,6-D24
250 uMRNA (103-MER)A-8D, C-D, G-8D, U-D5
250 uMRNA (103-MER)A-H, C-D, G-H, U-D6
250 uMRNA (103-MER)A-H, C-H, G-D, U-D7
Sample conditionsIonic strength: 3 mM / Label: condition_1 / pH: 7.5 pD / Pressure: 1 atm / Temperature: 308 K

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Data collection

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Refinement
MethodSoftware ordinalDetails
molecular dynamics4Structure minimization
distance geometry2The SAXS scattering profiles for each structure were back calculated and the structures with lowest chi2 compared with experimental SAXS data were selected.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 1200 / Conformers submitted total number: 10

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