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- PDB-5j2w: Intermediate state lying on the pathway of release of Tat from HI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5j2w | ||||||
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Title | Intermediate state lying on the pathway of release of Tat from HIV-1 TAR. | ||||||
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![]() | VIRAL PROTEIN / TAR:Tat complex / RAM simulations / Residual dipolar couplings / intermediate excited state | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
![]() | Borkar, A.N. / Bardaro Jr., M.F. / Varani, G. / Vendruscolo, M. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.3 KB | Display | ![]() |
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PDB format | ![]() | 205.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 278.7 KB | Display | ![]() |
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Full document | ![]() | 405.8 KB | Display | |
Data in XML | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 1768.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#2: RNA chain | Mass: 9307.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: in vitro transcription vector pT7-Fluc(deltai) (others) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Sample state: anisotropic / Type: Not applicable |
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Sample preparation
Details | Type: solution Contents: 2 uM [U-99% 13C; U-99% 15N] TAR and Tatp, 100% D2O Label: TAR:Tatp / Solvent system: 100% D2O |
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Sample | Conc.: 2 uM / Component: TAR and Tatp / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Ionic strength: 10 mM / Label: conditions_1 / pH: 6.6 / Pressure: 1 atm / Temperature: 298.15 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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Processing
NMR software | Name: ![]() |
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Refinement | Method: molecular dynamics / Software ordinal: 1 / Details: Replica averaged metadynamics (RAM) simulations |
NMR representative | Selection criteria: target function |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 3871 / Conformers submitted total number: 10 |