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- PDB-5j0m: Ground state sampled during RDC restrained Replica-averaged Metad... -

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Basic information

Entry
Database: PDB / ID: 5j0m
TitleGround state sampled during RDC restrained Replica-averaged Metadynamics (RAM) simulations of the HIV-1 TAR complexed with cyclic peptide mimetic of Tat
Components
  • Apical region (29-mer) of the HIV-1 TAR RNA element
  • Cyclic peptide mimetic of HIV-1 Tat
KeywordsVIRAL PROTEIN / TAR:Tat complex / RAM simulations / Residual dipolar couplings / ground state
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / molecular dynamics
AuthorsBorkar, A.N. / Bardaro Jr., M.F. / Varani, G. / Vendruscolo, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Dr Manmohan Singh Scholarship United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of a low-population binding intermediate in protein-RNA recognition.
Authors: Borkar, A.N. / Bardaro, M.F. / Camilloni, C. / Aprile, F.A. / Varani, G. / Vendruscolo, M.
History
DepositionMar 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Database references
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.5Oct 23, 2019Group: Data collection / Experimental preparation / Category: pdbx_nmr_exptl_sample_conditions
Item: _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_exptl_sample_conditions.temperature_units

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclic peptide mimetic of HIV-1 Tat
B: Apical region (29-mer) of the HIV-1 TAR RNA element


Theoretical massNumber of molelcules
Total (without water)11,0762
Polymers11,0762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1710 Å2
ΔGint-4 kcal/mol
Surface area6110 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 42217Lowest
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cyclic peptide mimetic of HIV-1 Tat


Mass: 1768.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#2: RNA chain Apical region (29-mer) of the HIV-1 TAR RNA element


Mass: 9307.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: anisotropic / Type: not applicable

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Sample preparation

DetailsType: solution
Contents: 2.0 uM [U-99% 13C; U-99% 15N] Apical region (29-mer) of the HIV-1 TAR RNA element, 2.0 uM [U-99% 13C; U-99% 15N] Cyclic peptide mimetic of HIV-1 Tat, 17 mg/mL Pf1 phage, 100% D2O
Label: TAR:Tatp / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 uMApical region (29-mer) of the HIV-1 TAR RNA element[U-99% 13C; U-99% 15N]1
2.0 uMCyclic peptide mimetic of HIV-1 Tat[U-99% 13C; U-99% 15N]1
17 mg/mLPf1 phagenatural abundance1
Sample conditionsIonic strength: 10 mM / Label: conditions_1 / pH: 6.6 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
Gromacs, PlumedVendruscolo, Camilloni and othersstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 2 / Details: RAM simulations
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Lowest / Conformers calculated total number: 42217 / Conformers submitted total number: 10

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