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Yorodumi- PDB-5j2w: Intermediate state lying on the pathway of release of Tat from HI... -
+Open data
-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. | ||||||
Components |
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Keywords | VIRAL PROTEIN / TAR:Tat complex / RAM simulations / Residual dipolar couplings / intermediate excited state | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Borkar, A.N. / Bardaro Jr., M.F. / Varani, G. / Vendruscolo, M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j2w.cif.gz | 258.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j2w.ent.gz | 198.8 KB | Display | PDB format |
PDBx/mmJSON format | 5j2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j2w_validation.pdf.gz | 433.8 KB | Display | wwPDB validaton report |
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Full document | 5j2w_full_validation.pdf.gz | 614.4 KB | Display | |
Data in XML | 5j2w_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 5j2w_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/5j2w ftp://data.pdbj.org/pub/pdb/validation_reports/j2/5j2w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Human immunodeficiency virus 1 |
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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.) Human immunodeficiency virus 1 Production host: in vitro transcription vector pT7-Fluc(deltai) (others) |
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Sample state: anisotropic / Type: Not applicable |
-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: Gromacs, Plumed / Developer: Vendruscolo, Camilloni, Borkar and others / Classification: structure calculation |
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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 |