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Open data
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Basic information
Entry | Database: PDB / ID: 2ldl | ||||||
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Title | Solution NMR Structure of the HIV-1 Exon Splicing Silencer 3 | ||||||
![]() | RNA (27-MER) | ||||||
![]() | RNA / exon splicing silencer | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
![]() | Mishler, C. / Levengood, J.D. / Johnson, C.A. / Rajan, P. / Znosko, B.M. | ||||||
![]() | ![]() Title: Solution Structure of the HIV-1 Exon Splicing Silencer 3. Authors: Levengood, J.D. / Rollins, C. / Mishler, C.H. / Johnson, C.A. / Miner, G. / Rajan, P. / Znosko, B.M. / Tolbert, B.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.3 KB | Display | ![]() |
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PDB format | ![]() | 172.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 324.8 KB | Display | ![]() |
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Full document | ![]() | 378.7 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 20.2 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: 8650.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 1-2 mM RNA (27-MER), 0.5-1 mM [U-100% 15N] RNA (27-MER), 0.5-1 mM [U-100% 13C] RNA (27-MER), 0.5-1 mM [U-2H] RNA (27-MER), 120 mM potassium chloride, 20 mM potassium phosphate, 10 mM ...Contents: 1-2 mM RNA (27-MER), 0.5-1 mM [U-100% 15N] RNA (27-MER), 0.5-1 mM [U-100% 13C] RNA (27-MER), 0.5-1 mM [U-2H] RNA (27-MER), 120 mM potassium chloride, 20 mM potassium phosphate, 10 mM cacodylate, 0.5 mM EDTA, 100% D2O Solvent system: 100% D2O | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 150 / pH: 5.5 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||
NMR constraints | NOE constraints total: 362 / NOE intraresidue total count: 170 / NOE long range total count: 18 / NOE sequential total count: 174 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 256 / Conformers submitted total number: 12 |