+Open data
-Basic information
Entry | Database: PDB / ID: 5vay | ||||||
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Title | Bcl-2 complex with Beclin 1 T108D BH3 domain | ||||||
Components |
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Keywords | APOPTOSIS / Bcl-2 / autophagy / Beclin 1 | ||||||
Function / homology | Function and homology information cellular response to aluminum ion / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development ...cellular response to aluminum ion / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / phosphatidylinositol 3-kinase complex, class III / positive regulation of melanocyte differentiation / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / response to mitochondrial depolarisation / mesenchymal cell development / retinal cell programmed cell death / positive regulation of attachment of mitotic spindle microtubules to kinetochore / positive regulation of neuron maturation / cytoplasmic side of mitochondrial outer membrane / negative regulation of osteoblast proliferation / negative regulation of lysosome organization / gland morphogenesis / positive regulation of autophagosome assembly / engulfment of apoptotic cell / renal system process / apoptotic process in bone marrow cell / negative regulation of autophagosome assembly / regulation of cell-matrix adhesion / T cell apoptotic process / stem cell development / receptor catabolic process / negative regulation of calcium ion transport into cytosol / melanocyte differentiation / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / ear development / lymphoid progenitor cell differentiation / dendritic cell proliferation / suppression by virus of host autophagy / protein targeting to lysosome / positive regulation of mononuclear cell proliferation / negative regulation of myeloid cell apoptotic process / early endosome to late endosome transport / cellular response to nitrogen starvation / negative regulation of epithelial cell apoptotic process / late endosome to vacuole transport / regulation of nitrogen utilization / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / glomerulus development / B cell apoptotic process / negative regulation of T cell apoptotic process / negative regulation of dendritic cell apoptotic process / oocyte development / negative regulation of execution phase of apoptosis / positive regulation of multicellular organism growth / neuron maturation / SMAD protein signal transduction / metanephros development / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of viral genome replication / negative regulation of motor neuron apoptotic process / focal adhesion assembly / endoplasmic reticulum calcium ion homeostasis / phagophore assembly site / negative regulation of ossification / fertilization / Translation of Replicase and Assembly of the Replication Transcription Complex / negative regulation of B cell apoptotic process / response to iron(II) ion / negative regulation of programmed cell death / response to UV-B / response to iron ion / negative regulation of protein localization to plasma membrane / regulation of mitochondrial membrane permeability / regulation of growth / calcium ion transport into cytosol / negative regulation of mitochondrial depolarization / channel activity / motor neuron apoptotic process / axon regeneration / Bcl-2 family protein complex / epithelial cell apoptotic process / smooth muscle cell migration / phosphatidylinositol-3-phosphate biosynthetic process / intrinsic apoptotic signaling pathway in response to oxidative stress / NFE2L2 regulating tumorigenic genes / Macroautophagy / digestive tract morphogenesis / response to cycloheximide / mitotic metaphase chromosome alignment / organ growth / branching involved in ureteric bud morphogenesis / cellular response to organic substance Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å | ||||||
Authors | Lee, E.F. / Smith, B.J. / Yao, S. / Fairlie, W.D. | ||||||
Citation | Journal: To Be Published Title: Bcl-2 complex with Beclin 1 pT108 BH3 domain Authors: Lee, E.F. / Smith, B.J. / Yao, S. / Fairlie, W.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vay.cif.gz | 285.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vay.ent.gz | 232.6 KB | Display | PDB format |
PDBx/mmJSON format | 5vay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/5vay ftp://data.pdbj.org/pub/pdb/validation_reports/va/5vay | HTTPS FTP |
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-Related structure data
Related structure data | 5vaxC 2xa0S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 19501.686 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2, BCL2L1, BCL2L, BCLX / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P10415, UniProt: Q07817 #2: Protein/peptide | Mass: 2859.177 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14457 #3: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Tris, pH 6.5, 0.2M ammonium acetate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 71186 / % possible obs: 98.95 % / Redundancy: 3.7 % / Net I/σ(I): 14.41 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XA0 Resolution: 1.804→50 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.804→50 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: 78.0455 Å / Origin y: 8.1132 Å / Origin z: 22.4968 Å
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Refinement TLS group | Selection details: all |