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Yorodumi- PDB-6trr: Structural insight into tanapoxvirus mediated inhibition of apoptosis -
+Open data
-Basic information
Entry | Database: PDB / ID: 6trr | |||||||||
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Title | Structural insight into tanapoxvirus mediated inhibition of apoptosis | |||||||||
Components |
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Keywords | APOPTOSIS / Pox virus / Bcl-2 | |||||||||
Function / homology | Function and homology information T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation ...T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / development of secondary sexual characteristics / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / B cell homeostatic proliferation / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / apoptotic process involved in blood vessel morphogenesis / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / Transcriptional regulation by RUNX2 / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / positive regulation of epithelial cell apoptotic process / calcium ion transport into cytosol / motor neuron apoptotic process / mitochondrial fusion / channel activity / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / hypothalamus development / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / BH3 domain binding / germ cell development / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / B cell homeostasis / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway by p53 class mediator / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / ectopic germ cell programmed cell death / cellular response to unfolded protein / blood vessel remodeling / Pyroptosis / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway in absence of ligand / response to salt stress / Hsp70 protein binding / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / negative regulation of protein binding / kidney development / response to gamma radiation / apoptotic signaling pathway / neuron migration / positive regulation of protein-containing complex assembly / response to toxic substance / cerebral cortex development / cellular response to virus / activation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process Similarity search - Function | |||||||||
Biological species | Yaba-like disease virus Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1200735104 Å | |||||||||
Authors | Suraweera, C.D. / Hinds, M.G. / Kvansakul, M. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Febs J. / Year: 2020 Title: Structural insight into tanapoxvirus-mediated inhibition of apoptosis. Authors: Suraweera, C.D. / Anasir, M.I. / Chugh, S. / Javorsky, A. / Impey, R.E. / Hasan Zadeh, M. / Soares da Costa, T.P. / Hinds, M.G. / Kvansakul, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6trr.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6trr.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 6trr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/6trr ftp://data.pdbj.org/pub/pdb/validation_reports/tr/6trr | HTTPS FTP |
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-Related structure data
Related structure data | 6tqpC 6tqqC 4uf1S 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
#1: Protein | Mass: 17442.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Tanapox virus Bcl-2 protein / Source: (gene. exp.) Yaba-like disease virus / Gene: 16L / Cell line (production host): C41 DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DHU6 | ||||
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#2: Protein/peptide | Mass: 3152.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BH3 motif of Human Bax protein / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07812 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.24 % / Description: single square bipyramidal shape crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 1.0 M Lithium Chloride, 0.1 M Citrate pH 4.0 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→42.31 Å / Num. obs: 11903 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 50.7844344791 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.12→2.18 Å / Num. unique obs: 946 / CC1/2: 0.291 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UF1 Resolution: 2.1200735104→33.6224352648 Å / SU ML: 0.307808956948 / Cross valid method: FREE R-VALUE / σ(F): 1.33600998648 / Phase error: 30.2921234659
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.773837679 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1200735104→33.6224352648 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 3.63385323757 Å / Origin y: 8.30386774601 Å / Origin z: 20.5216577962 Å
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Refinement TLS group | Selection details: all |