[English] 日本語
Yorodumi- PDB-2d19: Solution RNA structure of loop region of the HIV-1 dimerization i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d19 | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Solution RNA structure of loop region of the HIV-1 dimerization initiation site in the kissing-loop dimer | ||||||||||||||||||||
Components | 5'-R(*Keywords | RNA / DIS / HIV-1 | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing | Model type details | minimized average | Authors | Baba, S. / Takahashi, K. / Noguchi, S. / Takaku, H. / Koyanagi, Y. / Yamamoto, N. / Kawai, G. | Citation | Journal: J.Biochem.(Tokyo) / Year: 2005 | Title: Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. Authors: Baba, S. / Takahashi, K. / Noguchi, S. / Takaku, H. / Koyanagi, Y. / Yamamoto, N. / Kawai, G. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2d19.cif.gz | 233.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2d19.ent.gz | 193.9 KB | Display | PDB format |
PDBx/mmJSON format | 2d19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d19_validation.pdf.gz | 329.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2d19_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | 2d19_validation.xml.gz | 6 KB | Display | |
Data in CIF | 2d19_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/2d19 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/2d19 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: RNA chain | Mass: 5481.341 Da / Num. of mol.: 2 / Source method: obtained synthetically |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||||||||||||||||||
NMR details | Text: Chemical synthesized 25-mer RNA corresponding to the HIV-1 dimerization initiation site. Enzymatical synthesized [G-13C/15N] labeled 39-mer RNA corresponding to the HIV-1 dimerization ...Text: Chemical synthesized 25-mer RNA corresponding to the HIV-1 dimerization initiation site. Enzymatical synthesized [G-13C/15N] labeled 39-mer RNA corresponding to the HIV-1 dimerization initiation site. Enzymatical synthesized [A-13C/15N] labeled 39-mer RNA corresponding to the HIV-1 dimerization initiation site. Enzymatical synthesized 39-mer RNA corresponding to the HIV-1 dimerization initiation site. |
-Sample preparation
Details |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample conditions |
|
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structures are based on a total of 502 restraints, 286 are NOE-derived distance constraints, 140 dihedral angle restraints, 76 distance restraints from hydrogen bonds. | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 11 |