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Yorodumi- PDB-1pjy: Solution structure of the HIV-1 frameshift inducing stem-loop RNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pjy | ||||||
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Title | Solution structure of the HIV-1 frameshift inducing stem-loop RNA | ||||||
Components | HIV-1 frameshift inducing stem-loop | ||||||
Keywords | RNA / frameshift / HIV / tetraloop / RNA structure | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / torsion angle molecular dynamics, Cartesian space simulated annealing, molecular dynamics, residual dipolar coupling | ||||||
Authors | Staple, D.W. / Butcher, S.E. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2003 Title: Solution structure of the HIV-1 frameshift inducing stem-loop RNA. Authors: Staple, D.W. / Butcher, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pjy.cif.gz | 268.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pjy.ent.gz | 227.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pjy_validation.pdf.gz | 316.5 KB | Display | wwPDB validaton report |
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Full document | 1pjy_full_validation.pdf.gz | 427.7 KB | Display | |
Data in XML | 1pjy_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1pjy_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/1pjy ftp://data.pdbj.org/pub/pdb/validation_reports/pj/1pjy | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 7071.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 RNA transcript from synthetic DNA |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The incorporation of residual dipolar couplings and the direct detection of hydrogen bonds with HNN-COSY were used in solving this structure |
-Sample preparation
Details | Contents: 1 mM HIV-1 frameshift inducing stem-loop RNA / Solvent system: 90% H2O/10% D2O, or 99.99% D2O | ||||||||||||||||||||
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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 |
-Processing
NMR software |
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Refinement | Method: torsion angle molecular dynamics, Cartesian space simulated annealing, molecular dynamics, residual dipolar coupling Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: Submitted confermers represent the 20 lowest energy structures with no NOE violations greater than 0.2 Angstroms and no dihedral violations greater than 5 degrees Conformers calculated total number: 100 / Conformers submitted total number: 20 |