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- PDB-7t1p: Solution structure of 7SK stem-loop 1 with HIV-1 Tat Finland Argi... -

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Basic information

Entry
Database: PDB / ID: 7t1p
TitleSolution structure of 7SK stem-loop 1 with HIV-1 Tat Finland Arginine Rich Motif
Components
  • RNA (56-MER)
  • Tat Finland Arginine Rich Motif
KeywordsTRANSCRIPTION / Tat / 7SK / HIV-1
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
HIV-1 06TG.HT008 (virus)
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing
AuthorsPham, V.V. / Gao, M. / D'Souza, V.M.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)55108516 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI50470 United States
CitationJournal: Commun Biol / Year: 2022
Title: A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA.
Authors: Pham, V.V. / Gao, M. / Meagher, J.L. / Smith, J.L. / D'Souza, V.M.
History
DepositionDec 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1May 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 (56-MER)
B: Tat Finland Arginine Rich Motif


Theoretical massNumber of molelcules
Total (without water)20,1312
Polymers20,1312
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (56-MER)


Mass: 17986.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein/peptide Tat Finland Arginine Rich Motif


Mass: 2144.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HIV-1 06TG.HT008 (virus)

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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
222isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM 7SK-SL1, 0.5 mM Tat Fin, 100% D2OTatFin:7SK D2O100% D2O
solution20.5 mM 7SK-SL1, 0.5 mM Tat Fin, 90% H2O/10% D2OTatFin:7SK H2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mM7SK-SL1natural abundance1
0.5 mMTat Finnatural abundance1
0.5 mM7SK-SL1natural abundance2
0.5 mMTat Finnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
110mM Phosphate, 70mM NaCl, 0.1mM EDTA mMTatFin:7SK D2O5.6 100000 Pa298 K
210mM Phosphate, 70mM NaCl, 0.1mM EDTA mMTatFin:7SK H2O5.6 100000 Pa298 K

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Data collection

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz
Soln scatterType: neutron / Buffer name: 10 mM phosphate, 70 mM NaCl, 0.1 mM EDTA / Data analysis software list: Scatter / Data reduction software list: ATSAS / Detector specific: Dectris / Detector type: Pilatus3 X 2M detector / Mean guiner radius: 2.5 nm / Num. of time frames: 10 / Sample pH: 5.6 / Source beamline: 12.3.1 / Source beamline instrument: SIBYLS / Source class: Y / Source type: 12.3.1 (SIBYLS) beam line / Temperature: 283 K

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10
Soln scatter modelMethod: This structure was calculated with XPLOR-NIH with a CYANA input and minimized with SAXS.

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