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Yorodumi- PDB-6mcf: Solution structure of 7SK stem-loop 1 with HIV-1 Tat RNA Binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mcf | |||||||||
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Title | Solution structure of 7SK stem-loop 1 with HIV-1 Tat RNA Binding Domain | |||||||||
Components |
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Keywords | TRANSCRIPTION / RNA Binding Domain / RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information trans-activation response element binding / Interactions of Tat with host cellular proteins / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / evasion of host immune response / molecular sequestering activity / host cell nucleolus / actinin binding ...trans-activation response element binding / Interactions of Tat with host cellular proteins / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / evasion of host immune response / molecular sequestering activity / host cell nucleolus / actinin binding / negative regulation of peptidyl-threonine phosphorylation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Tat-mediated elongation of the HIV-1 transcript / RNA-binding transcription regulator activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / PKR-mediated signaling / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / protein domain specific binding / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus type 1 group M subtype B | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
Authors | Pham, V.V. / D'Souza, V.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry. Authors: Pham, V.V. / Salguero, C. / Khan, S.N. / Meagher, J.L. / Brown, W.C. / Humbert, N. / de Rocquigny, H. / 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 | 6mcf.cif.gz | 426.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mcf.ent.gz | 351.7 KB | Display | PDB format |
PDBx/mmJSON format | 6mcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mcf_validation.pdf.gz | 419.9 KB | Display | wwPDB validaton report |
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Full document | 6mcf_full_validation.pdf.gz | 535.1 KB | Display | |
Data in XML | 6mcf_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 6mcf_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/6mcf ftp://data.pdbj.org/pub/pdb/validation_reports/mc/6mcf | HTTPS FTP |
-Related structure data
Related structure data | 6mceC 6mciC C: citing same article (ref.) |
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Similar structure data | |
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: 18358.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#2: Protein/peptide | Mass: 2162.533 Da / Num. of mol.: 1 / Fragment: RNA BINDING DOMAIN RESIDUES 44-60 / Source method: obtained synthetically Source: (synth.) Human immunodeficiency virus type 1 group M subtype B References: UniProt: P04608 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 10mM phosphates, 70mM NaCl mM / Label: 7SK_conditions / pH: 5.4 / Pressure: 100000 Pa / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 6 | ||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 20 / Conformers submitted total number: 10 |