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Yorodumi- PDB-7qtx: Kaposi sarcoma associated herpes virus (KSHV) encoded apoptosis i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qtx | ||||||
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Title | Kaposi sarcoma associated herpes virus (KSHV) encoded apoptosis inhibitor, KsBcl-2 in complex with Puma BH3 | ||||||
Components |
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Keywords | APOPTOSIS / viral Bcl-2 protein / gamma herpes virus / Kaposi sarcoma virus | ||||||
Function / homology | Function and homology information positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / symbiont-mediated suppression of host apoptosis / negative regulation of growth / positive regulation of fibroblast apoptotic process / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of cysteine-type endopeptidase activity / positive regulation of thymocyte apoptotic process / fibroblast apoptotic process ...positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / symbiont-mediated suppression of host apoptosis / negative regulation of growth / positive regulation of fibroblast apoptotic process / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of cysteine-type endopeptidase activity / positive regulation of thymocyte apoptotic process / fibroblast apoptotic process / execution phase of apoptosis / Activation of PUMA and translocation to mitochondria / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / cellular response to ionizing radiation / determination of adult lifespan / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to hypoxia / regulation of apoptotic process / mitochondrial outer membrane / DNA damage response / mitochondrion / membrane / cytosol Similarity search - Function | ||||||
Biological species | Human gammaherpesvirus 8 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11598861103 Å | ||||||
Authors | Suraweera, C.D. / Hinds, M.G. / Kvansakul, M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Viruses / Year: 2022 Title: Structural Insight into KsBcl-2 Mediated Apoptosis Inhibition by Kaposi Sarcoma Associated Herpes Virus. Authors: Suraweera, C.D. / 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 | 7qtx.cif.gz | 133.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qtx.ent.gz | 87.2 KB | Display | PDB format |
PDBx/mmJSON format | 7qtx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qtx_validation.pdf.gz | 442.6 KB | Display | wwPDB validaton report |
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Full document | 7qtx_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 7qtx_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 7qtx_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/7qtx ftp://data.pdbj.org/pub/pdb/validation_reports/qt/7qtx | HTTPS FTP |
-Related structure data
Related structure data | 7qtwC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16637.180 Da / Num. of mol.: 1 / Mutation: V117A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human gammaherpesvirus 8 / Gene: ORF16, HHV8GK18_gp19 / Production host: Escherichia coli (E. coli) / Variant (production host): Codon plus (RIL) / References: UniProt: Q76RI8 | ||||||
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#2: Protein/peptide | Mass: 3210.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXH1 | ||||||
#3: Chemical | #4: Chemical | #5: 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: 2.06 Å3/Da / Density % sol: 40.41 % / Description: single long rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M sodium bromide, 0.1 M Bis-tris propane pH 6.5, 20% PEG 3350 |
-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: 0.937 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.937 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→32.4632234192 Å / Num. obs: 9148 / % possible obs: 98.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 32.4290222293 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.11→2.17 Å / Num. unique obs: 409 / CC1/2: 0.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: KsBcl-2_Bid Resolution: 2.11598861103→32.4632234192 Å / SU ML: 0.312535587486 / Cross valid method: FREE R-VALUE / σ(F): 1.35034511599 / Phase error: 30.1945594635 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.4042455698 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11598861103→32.4632234192 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: 6.14585868528 Å / Origin y: 33.5559067189 Å / Origin z: 13.458405656 Å
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Refinement TLS group | Selection details: all |