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Yorodumi- PDB-4or5: Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4or5 | ||||||
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Title | Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4 | ||||||
Components |
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Keywords | Transferase/Transcription / Cdk9 / Tat / AFF4 / Zinc Finger / Transcription / RNA binding / Phosphorylation / Transferase-Transcription 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 / protein serine/threonine phosphatase inhibitor activity / 7SK snRNA binding / positive regulation of viral transcription / 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 / protein serine/threonine phosphatase inhibitor activity / 7SK snRNA binding / positive regulation of viral transcription / 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 / evasion of host immune response / molecular sequestering activity / nucleus localization / host cell nucleolus / actinin binding / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / negative regulation of protein localization to chromatin / positive regulation of DNA-templated transcription, elongation / RNA polymerase binding / [RNA-polymerase]-subunit kinase / transcription elongation-coupled chromatin remodeling / replication fork processing / negative regulation of peptidyl-threonine phosphorylation / regulation of cyclin-dependent protein serine/threonine kinase activity / spermatid development / cellular response to cytokine stimulus / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA-binding transcription regulator activity / Tat-mediated elongation of the HIV-1 transcript / 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 / response to endoplasmic reticulum stress / cyclin binding / molecular condensate scaffold activity / RNA polymerase II CTD heptapeptide repeat kinase activity / transcription elongation factor complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / euchromatin / PKR-mediated signaling / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / PML body / fibrillar center / 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 / response to xenobiotic stimulus / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / protein domain specific binding / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) HIV-1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Gu, J. / Babayeva, N.D. / Suwa, Y. / Baranovskiy, A.G. / Price, D.H. / Tahirov, T.H. | ||||||
Citation | Journal: Cell Cycle / Year: 2014 Title: Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4. Authors: Gu, J. / Babayeva, N.D. / Suwa, Y. / Baranovskiy, A.G. / Price, D.H. / Tahirov, T.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4or5.cif.gz | 279.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4or5.ent.gz | 232.7 KB | Display | PDB format |
PDBx/mmJSON format | 4or5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/4or5 ftp://data.pdbj.org/pub/pdb/validation_reports/or/4or5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 4 molecules AFBG
#1: Protein | Mass: 37544.574 Da / Num. of mol.: 2 / Fragment: UNP residues 7-332 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK9, CDC2L4, TAK References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase #2: Protein | Mass: 30877.320 Da / Num. of mol.: 2 / Fragment: UNP residues 1-226 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1 / References: UniProt: O60563 |
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-Protein/peptide , 2 types, 4 molecules CHEJ
#3: Protein/peptide | Mass: 5428.422 Da / Num. of mol.: 2 / Fragment: UNP residues 1-48 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV-1 (virus) / Strain: isolate HXB2 / Gene: tat / References: UniProt: P04608 #4: Protein/peptide | Mass: 4887.460 Da / Num. of mol.: 2 / Fragment: UNP residues 32-69 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AFF4, AF5Q31, MCEF, HSPC092 / References: UniProt: Q9UHB7 |
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-Non-polymers , 4 types, 124 molecules
#5: Chemical | ChemComp-YT3 / #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-ZN / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.64 Å3/Da / Density % sol: 73.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50 mM MES pH6.5, 3.7-3.75% w/v PEG 20000, 5 mM YCl3, 200 mM NDSB 211, 2 mM TCEP pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2013 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 67551 / Num. obs: 67551 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.2 / % possible all: 87.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→41.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 5136435.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.6498 Å2 / ksol: 0.312516 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→41.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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