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- PDB-1osw: The Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1osw | ||||||||||||||||||
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Title | The Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein Binding for a 1X3 Internal Loop | ||||||||||||||||||
![]() | 5'-R(*![]() RNA | Function / homology | RNA / RNA (> 10) | ![]() Method | SOLUTION NMR / DYANA, molecular dynamics using AMBER | ![]() Yuan, Y. / Kerwood, D.J. / Paoletti, A.C. / Shubsda, M.F. / Borer, P.N. | ![]() ![]() Title: Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein Binding for a 1X3 Internal Loop Authors: Yuan, Y. / Kerwood, D.J. / Paoletti, A.C. / Shubsda, M.F. / Borer, P.N. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 294.6 KB | Display | ![]() |
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PDB format | ![]() | 253.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 325.1 KB | Display | ![]() |
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Full document | ![]() | 445 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 12.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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: RNA chain | Mass: 7472.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA sequence obtained from Dharmacon |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: Structures were determined using 2D NOESY at different temperatures and mixing times. The last residue, A23, was eliminated from the pdb file due to ambiguity in orientation. |
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Sample preparation
Details | Contents: 1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3 Solvent system: 99.996% D2O or 90% D2O, 10% H2O | |||||||||||||||
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: DYANA, molecular dynamics using AMBER / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy,target function Conformers calculated total number: 50 / Conformers submitted total number: 23 |