+Open data
-Basic information
Entry | Database: PDB / ID: 6cyt | ||||||
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Title | HIV-1 TAR loop in complex with Tat:AFF4:P-TEFb | ||||||
Components |
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Keywords | TRANSCRIPTION/RNA / RNA binding protein / HIV-1 Tat / transcription elongation / HIV-1 TAR / TRANSCRIPTION / TRANSCRIPTION-RNA complex | ||||||
Function / homology | Function and homology information super elongation complex / trans-activation response element binding / P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing ...super elongation complex / trans-activation response element binding / P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / nucleus localization / evasion of host immune response / molecular sequestering activity / host cell nucleolus / actinin binding / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / positive regulation of DNA-templated transcription, elongation / RNA polymerase binding / [RNA-polymerase]-subunit kinase / negative regulation of protein localization to chromatin / transcription elongation-coupled chromatin remodeling / regulation of cyclin-dependent protein serine/threonine kinase activity / replication fork processing / negative regulation of peptidyl-threonine phosphorylation / cellular response to cytokine stimulus / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / spermatid development / Tat-mediated elongation of the HIV-1 transcript / RNA-binding transcription regulator activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / regulation of DNA repair / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / viral process / response to endoplasmic reticulum stress / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / molecular condensate scaffold activity / transcription elongation factor complex / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / euchromatin / PKR-mediated signaling / PML body / fibrillar center / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / kinase activity / regulation of gene expression / DNA-binding transcription factor binding / Estrogen-dependent gene expression / cell population proliferation / host cell cytoplasm / transcription by RNA polymerase II / transcription cis-regulatory region binding / regulation of cell cycle / protein kinase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / response to xenobiotic stimulus / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / virus-mediated perturbation of host defense response / protein serine/threonine kinase activity / DNA-templated transcription / chromatin binding / host cell nucleus / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Schulze Gahmen, U. / Hurley, J.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex. Authors: Schulze-Gahmen, U. / Hurley, J.H. #1: Journal: Elife / Year: 2016 Title: Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. Authors: Schulze-Gahmen, U. / Echeverria, I. / Stjepanovic, G. / Bai, Y. / Lu, H. / Schneidman-Duhovny, D. / Doudna, J.A. / Zhou, Q. / Sali, A. / Hurley, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cyt.cif.gz | 311 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cyt.ent.gz | 250.3 KB | Display | PDB format |
PDBx/mmJSON format | 6cyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cyt_validation.pdf.gz | 483.8 KB | Display | wwPDB validaton report |
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Full document | 6cyt_full_validation.pdf.gz | 487.1 KB | Display | |
Data in XML | 6cyt_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 6cyt_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/6cyt ftp://data.pdbj.org/pub/pdb/validation_reports/cy/6cyt | HTTPS FTP |
-Related structure data
Related structure data | 5l1zS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ABD
#1: Protein | Mass: 38226.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK9, CDC2L4, TAK Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
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#2: Protein | Mass: 30618.959 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1 Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) References: UniProt: O60563 |
#4: Protein | Mass: 6784.110 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: tat Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths) References: UniProt: A0A0C5HAL9, UniProt: P04608*PLUS |
-Protein/peptide / RNA chain / Non-polymers , 3 types, 4 molecules CN
#3: Protein/peptide | Mass: 4164.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AFF4, AF5Q31, MCEF, HSPC092 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHB7 |
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#5: RNA chain | Mass: 6438.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 |
#6: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.13 Å3/Da / Density % sol: 70.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 50 mM Tris 8.5, 0.2M Ammonium Acetate, 6 mM MgCl2, 8% PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 11, 2017 |
Radiation | Monochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11583 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→140 Å / Num. obs: 17145 / % possible obs: 99.47 % / Redundancy: 37.6 % / CC1/2: 0.999 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 3.5→3.625 Å / Redundancy: 16.3 % / Mean I/σ(I) obs: 0.63 / Num. unique obs: 1690 / CC1/2: 0.441 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L1Z Resolution: 3.5→128.674 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 329.53 Å2 / Biso mean: 154.237 Å2 / Biso min: 82.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→128.674 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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