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Yorodumi- PDB-2d1a: Solution RNA structure model of the HIV-1 dimerization initiation... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d1a | ||||||
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Title | Solution RNA structure model of the HIV-1 dimerization initiation site in the extended-duplex dimer | ||||||
Components | RNA | ||||||
Keywords | RNA / DIS / HIV-1 | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / minimization of model RNA | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d1a.cif.gz | 59.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d1a.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 2d1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d1a_validation.pdf.gz | 299.5 KB | Display | wwPDB validaton report |
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Full document | 2d1a_full_validation.pdf.gz | 299.4 KB | Display | |
Data in XML | 2d1a_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 2d1a_validation.cif.gz | 3.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/2d1a ftp://data.pdbj.org/pub/pdb/validation_reports/d1/2d1a | 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: RNA chain | Mass: 12654.604 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: model structure was constructed by combining the structure parts |
-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: Discover / Version: 97 / Developer: Accelrys / Classification: refinement |
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Refinement | Method: minimization of model RNA / Software ordinal: 1 Details: Solution structures of DIS39 were constructed by combining the structure parts. Structures of the loop region of the extended-duplex dimer (2D18) and stem-bulge-stem region (2D17) were ...Details: Solution structures of DIS39 were constructed by combining the structure parts. Structures of the loop region of the extended-duplex dimer (2D18) and stem-bulge-stem region (2D17) were combined by superimposing the two base pairs, C12:G26 and U13:G25. |
NMR representative | Selection criteria: model structure |
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 1 / Conformers submitted total number: 1 |