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Yorodumi- PDB-7t1p: Solution structure of 7SK stem-loop 1 with HIV-1 Tat Finland Argi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t1p | |||||||||
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Title | Solution structure of 7SK stem-loop 1 with HIV-1 Tat Finland Arginine Rich Motif | |||||||||
Components |
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Keywords | TRANSCRIPTION / Tat / 7SK / HIV-1 | |||||||||
Function / homology | RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | Homo sapiens (human) HIV-1 06TG.HT008 (virus) | |||||||||
Method | SOLUTION NMR / SOLUTION SCATTERING / simulated annealing | |||||||||
Authors | Pham, V.V. / Gao, M. / D'Souza, V.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Commun Biol / Year: 2022 Title: A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA. Authors: Pham, V.V. / Gao, M. / Meagher, J.L. / Smith, J.L. / D'Souza, V.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t1p.cif.gz | 409.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t1p.ent.gz | 342.1 KB | Display | PDB format |
PDBx/mmJSON format | 7t1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/7t1p ftp://data.pdbj.org/pub/pdb/validation_reports/t1/7t1p | HTTPS FTP |
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-Related structure data
Related structure data | 7t1nC 7t1oC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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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: 17986.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#2: Protein/peptide | Mass: 2144.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HIV-1 06TG.HT008 (virus) |
-Experimental details
-Experiment
Experiment |
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions |
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-Data collection
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz |
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Soln scatter | Type: neutron / Buffer name: 10 mM phosphate, 70 mM NaCl, 0.1 mM EDTA / Data analysis software list: Scatter / Data reduction software list: ATSAS / Detector specific: Dectris / Detector type: Pilatus3 X 2M detector / Mean guiner radius: 2.5 nm / Num. of time frames: 10 / Sample pH: 5.6 / Source beamline: 12.3.1 / Source beamline instrument: SIBYLS / Source class: Y / Source type: 12.3.1 (SIBYLS) beam line / Temperature: 283 K |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 8 | |||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 | |||||||||||||||||||||||||||
Soln scatter model | Method: This structure was calculated with XPLOR-NIH with a CYANA input and minimized with SAXS. |