[English] 日本語
Yorodumi- PDB-3dvu: Crystal structure of the complex of murine gamma-herpesvirus 68 B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dvu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and the Beclin 1 BH3 domain | ||||||
Components |
| ||||||
Keywords | Viral Protein/apoptosis / AUTOPHAGY / PROTEIN-PROTEIN COMPLEX / VIRAL BCL-2 / BECLIN 1 / APOPTOSIS / M11 / ANTIVIRAL DEFENSE / BH3 DOMAIN / Coiled coil / Cytoplasm / Golgi apparatus / Membrane / Polymorphism / Viral Protein-apoptosis COMPLEX | ||||||
Function / homology | Function and homology information cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / : / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization ...cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / : / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / positive regulation of autophagosome assembly / engulfment of apoptotic cell / negative regulation of autophagosome assembly / receptor catabolic process / suppression by virus of host autophagy / protein targeting to lysosome / early endosome to late endosome transport / cellular response to nitrogen starvation / late endosome to vacuole transport / SMAD protein signal transduction / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / response to iron(II) ion / negative regulation of programmed cell death / phosphatidylinositol-3-phosphate biosynthetic process / Macroautophagy / mitotic metaphase chromosome alignment / lysosome organization / positive regulation of cardiac muscle hypertrophy / cytoplasmic pattern recognition receptor signaling pathway / p38MAPK cascade / autophagosome maturation / mitophagy / autophagosome assembly / autophagosome / neuron development / negative regulation of reactive oxygen species metabolic process / response to vitamin E / regulation of macroautophagy / cellular defense response / cellular response to glucose starvation / amyloid-beta metabolic process / phosphatidylinositol 3-kinase binding / phagocytic vesicle / positive regulation of autophagy / positive regulation of intrinsic apoptotic signaling pathway / JNK cascade / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / regulation of cytokinesis / regulation of autophagy / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to lead ion / trans-Golgi network / : / cellular response to hydrogen peroxide / ISG15 antiviral mechanism / autophagy / protein-macromolecule adaptor activity / GTPase binding / Translation of Replicase and Assembly of the Replication Transcription Complex / protein-containing complex assembly / regulation of apoptotic process / defense response to virus / host cell cytoplasm / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / molecular adaptor activity / nuclear body / endosome membrane / Ub-specific processing proteases / endosome / response to xenobiotic stimulus / cell division / negative regulation of cell population proliferation / dendrite / apoptotic process / ubiquitin protein ligase binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Murid herpesvirus 4 (Murine herpesvirus 68) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sinha, S. | ||||||
Citation | Journal: Autophagy / Year: 2008 Title: Molecular basis of the regulation of Beclin 1-dependent autophagy by the gamma-herpesvirus 68 Bcl-2 homolog M11. Authors: Sinha, S. / Colbert, C.L. / Becker, N. / Wei, Y. / Levine, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3dvu.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3dvu.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 3dvu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/3dvu ftp://data.pdbj.org/pub/pdb/validation_reports/dv/3dvu | HTTPS FTP |
---|
-Related structure data
Related structure data | 2aboS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16652.883 Da / Num. of mol.: 2 / Fragment: residues 2-136 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68) Gene: v-bcl-2, GAMMAHV.M11, M11 / Plasmid: pET21(d+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P89884 #2: Protein/peptide | Mass: 2845.193 Da / Num. of mol.: 2 / Fragment: BH3 domain, residues 105-130 / Source method: obtained synthetically Details: Peptide synthesis; The peptide corresponding to human Beclin 1 residues 105-130 was chemically synthesized. References: UniProt: Q14457 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.12 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% PEG 3350, 0.1M sodium acetate, pH 4.5, 10mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97874 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 16, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97874 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 22424 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.156 / Rsym value: 0.156 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1394 / Rsym value: 0.42 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ABO with residues 52-73 removed. Resolution: 2.5→19.7 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1493683.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.2445 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.5 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.7 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|