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Yorodumi- PDB-7p9w: Epstein-Barr virus encoded apoptosis regulator BHRF1 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p9w | ||||||
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Title | Epstein-Barr virus encoded apoptosis regulator BHRF1 in complex with Puma BH3 | ||||||
Components |
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Keywords | APOPTOSIS / BHRF-1 / Bcl-2 / Epstein-Barr 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 / negative regulation of growth / positive regulation of fibroblast apoptotic process / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host apoptosis / T cell apoptotic process / suppression by virus of host autophagy / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of cysteine-type endopeptidase activity ...positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host apoptosis / T cell apoptotic process / suppression by virus of host autophagy / 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 / Activation of PUMA and translocation to mitochondria / FOXO-mediated transcription of cell death genes / execution phase of apoptosis / negative regulation of release of cytochrome c from mitochondria / 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 / host cell mitochondrion / host cell membrane / 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 / determination of adult lifespan / cellular response to ionizing radiation / 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 / mitochondrial outer membrane / DNA damage response / apoptotic process / mitochondrion / membrane / cytosol Similarity search - Function | ||||||
Biological species | Epstein-Barr virus (Epstein-Barr virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00010064633 Å | ||||||
Authors | Suraweera, C.D. / Hinds, M.G. / Kvansakul, M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Viruses / Year: 2022 Title: Crystal Structures of Epstein-Barr Virus Bcl-2 Homolog BHRF1 Bound to Bid and Puma BH3 Motif Peptides. 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 | 7p9w.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p9w.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 7p9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p9w_validation.pdf.gz | 471.2 KB | Display | wwPDB validaton report |
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Full document | 7p9w_full_validation.pdf.gz | 472.6 KB | Display | |
Data in XML | 7p9w_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 7p9w_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/7p9w ftp://data.pdbj.org/pub/pdb/validation_reports/p9/7p9w | HTTPS FTP |
-Related structure data
Related structure data | 7p33C 2xpxS S: Starting model for refinement 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 19848.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8)) Strain: B95-8 / Gene: BHRF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03182 |
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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 |
-Non-polymers , 7 types, 79 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NH4 / | #6: Chemical | #7: Chemical | ChemComp-MG / #8: Chemical | ChemComp-CL / #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.36 Å3/Da / Density % sol: 47.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4 M Ammonium phosphate monobasic |
-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: Feb 9, 2021 |
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→46.88 Å / Num. obs: 14768 / % possible obs: 99.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 32.9318121567 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.992 / Num. unique obs: 1053 / CC1/2: 0.47 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XPX Resolution: 2.00010064633→35.2465186007 Å / SU ML: 0.219989114422 / Cross valid method: FREE R-VALUE / σ(F): 1.33751952487 / Phase error: 25.9130784494 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: 52.9736061707 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.00010064633→35.2465186007 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: 93.5433610824 Å / Origin y: -12.3516755543 Å / Origin z: 5.31897999283 Å
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Refinement TLS group | Selection details: all |