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- PDB-7p9w: Epstein-Barr virus encoded apoptosis regulator BHRF1 in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p9w | ||||||
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Title | Epstein-Barr virus encoded apoptosis regulator BHRF1 in complex with Puma BH3 | ||||||
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![]() | APOPTOSIS / BHRF-1 / Bcl-2 / Epstein-Barr virus | ||||||
Function / homology | ![]() 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 / 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 ...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 / 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 / execution phase of apoptosis / Activation of PUMA and translocation to mitochondria / FOXO-mediated transcription of cell death genes / 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 / 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 / mitochondrial outer membrane / DNA damage response / mitochondrion / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suraweera, C.D. / Hinds, M.G. / Kvansakul, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.4 KB | Display | ![]() |
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PDB format | ![]() | 95.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.2 KB | Display | ![]() |
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Full document | ![]() | 472.6 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p33C ![]() 2xpxS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() Strain: B95-8 / Gene: BHRF1 / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 3210.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 7 types, 79 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/PDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/PDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |