[English] 日本語
Yorodumi- PDB-7p0s: ORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p0s | ||||||
---|---|---|---|---|---|---|---|
Title | ORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 peptide | ||||||
Components |
| ||||||
Keywords | APOPTOSIS / ORF virus / Bcl-2 | ||||||
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 / 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 ...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 / 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 / mitochondrial outer membrane / DNA damage response / mitochondrion / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Orf virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.50315873146 Å | ||||||
Authors | Suraweera, C.D. / Hinds, M.G. / Kvansakul, M. | ||||||
Funding support | Australia, 1items
| ||||||
Citation | Journal: Viruses / Year: 2021 Title: Structural Investigation of Orf Virus Bcl-2 Homolog ORFV125 Interactions with BH3-Motifs from BH3-Only Proteins Puma and Hrk. Authors: Suraweera, C.D. / Hinds, M.G. / Kvansakul, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7p0s.cif.gz | 228.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7p0s.ent.gz | 155.7 KB | Display | PDB format |
PDBx/mmJSON format | 7p0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p0s_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7p0s_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 7p0s_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 7p0s_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/7p0s ftp://data.pdbj.org/pub/pdb/validation_reports/p0/7p0s | HTTPS FTP |
-Related structure data
Related structure data | 7p0uC 7adtS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16160.256 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Conserved Bcl-2 fold with 7 alpha helices / Source: (gene. exp.) Orf virus / Gene: ORFV125, ORF125 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A0R8HV90 #2: Protein/peptide | Mass: 3210.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Puma BH3 peptide 26-mer / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXH1 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.32 % / Description: Single rod shaped crystal |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium acetate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.503→43.283140319 Å / Num. obs: 11059 / % possible obs: 96.97 % / Redundancy: 4.1 % / Biso Wilson estimate: 62.9564032227 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Net I/σ(I): 8.91 |
Reflection shell | Resolution: 2.503→2.6 Å / Rmerge(I) obs: 1.35 / Num. unique obs: 1219 / CC1/2: 0.296 / % possible all: 98.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ADT Resolution: 2.50315873146→43.283140319 Å / SU ML: 0.43090510967 / Cross valid method: FREE R-VALUE / σ(F): 1.33792022765 / Phase error: 36.1923713478 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.50315873146→43.283140319 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 21.6252816749 Å / Origin y: 3.28902382585 Å / Origin z: 5.78428629941 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |