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Yorodumi- PDB-3mia: Crystal structure of HIV-1 Tat complexed with ATP-bound human P-TEFb -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mia | ||||||
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Title | Crystal structure of HIV-1 Tat complexed with ATP-bound human P-TEFb | ||||||
Components |
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Keywords | PROTEIN BINDING / P-TEFb / Cdk9 / Cyclin T1 / HIV-1 / Tat | ||||||
Function / homology | Function and homology information 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 ...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 / 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 / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / transcription elongation factor complex / molecular condensate scaffold activity / 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 / PKR-mediated signaling / PML body / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / kinase activity / 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 / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å | ||||||
Authors | Tahirov, T.H. / Babayeva, N.D. / Varzavand, K. / Cooper, J.J. / Sedore, S.C. / Price, D.H. | ||||||
Citation | Journal: Nature / Year: 2010 Title: Crystal structure of HIV-1 Tat complexed with human P-TEFb. Authors: Tahirov, T.H. / Babayeva, N.D. / Varzavand, K. / Cooper, J.J. / Sedore, S.C. / Price, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mia.cif.gz | 140.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mia.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 3mia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mia_validation.pdf.gz | 809.6 KB | Display | wwPDB validaton report |
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Full document | 3mia_full_validation.pdf.gz | 829.8 KB | Display | |
Data in XML | 3mia_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 3mia_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/3mia ftp://data.pdbj.org/pub/pdb/validation_reports/mi/3mia | HTTPS FTP |
-Related structure data
Related structure data | 3mi9SC S: Starting model for refinement C: citing same article (ref.) |
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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 ABC
#1: Protein | Mass: 40692.152 Da / Num. of mol.: 1 / Fragment: UNP residues 1-345, Protein kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC2L4, CDK9 / Plasmid: pENTR/SD/D-TOPO vector (Invitrogen K2420) / Cell (production host): insect cells / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
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#2: Protein | Mass: 30877.320 Da / Num. of mol.: 1 / Fragment: UNP residues 1-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1, Cyclin T1 / Plasmid: pENTR/SD/D-TOPO vector (Invitrogen K2420) / Cell (production host): insect cells / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: O60563 |
#3: Protein | Mass: 9848.327 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: isolate HXB2 group M subtype B / Gene: tat / Plasmid: pENTR/SD/D-TOPO vector (Invitrogen K2420) / Cell (production host): insect cells / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P04608 |
-Non-polymers , 4 types, 31 molecules
#4: Chemical | ChemComp-ANP / | ||
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#5: Chemical | ChemComp-MG / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50 mM HEPES buffer (pH 7.5), 4.25-5% PEG 20,000, 1 mM TCEP, and 20 mM glycyl-glycyl-glycine. The Tat P-TEFb ATP crystals were obtained by soaking the Tat P-TEFb crystals in crystallization ...Details: 50 mM HEPES buffer (pH 7.5), 4.25-5% PEG 20,000, 1 mM TCEP, and 20 mM glycyl-glycyl-glycine. The Tat P-TEFb ATP crystals were obtained by soaking the Tat P-TEFb crystals in crystallization solution with 1mM ATP analog AMPPNP and 5 mM magnesium chloride for 40 min., 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-C / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 19980 / % possible obs: 96.9 % / Observed criterion σ(I): -2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.7 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3mi9 Resolution: 3→30.61 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2849681.9 / 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: 26.7012 Å2 / ksol: 0.328984 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→30.61 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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