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Yorodumi- PDB-4s0o: Crystal Structure of the Autoinhibited Dimer of Pro-apoptotic BAX (I) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4s0o | ||||||
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Title | Crystal Structure of the Autoinhibited Dimer of Pro-apoptotic BAX (I) | ||||||
Components | Apoptosis regulator BAX | ||||||
Keywords | APOPTOSIS / BCL-2 FAMILY PROTEIN / APOPTOSIS REGULATOR / AUTOINHIBITED DIMER | ||||||
Function / homology | Function and homology information T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation ...T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / development of secondary sexual characteristics / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / B cell homeostatic proliferation / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / apoptotic process involved in blood vessel morphogenesis / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / Transcriptional regulation by RUNX2 / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / calcium ion transport into cytosol / motor neuron apoptotic process / mitochondrial fusion / channel activity / positive regulation of epithelial cell apoptotic process / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / hypothalamus development / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / BH3 domain binding / germ cell development / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / B cell homeostasis / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway by p53 class mediator / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / ectopic germ cell programmed cell death / cellular response to unfolded protein / blood vessel remodeling / Pyroptosis / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway in absence of ligand / response to salt stress / Hsp70 protein binding / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / negative regulation of protein binding / kidney development / apoptotic signaling pathway / response to gamma radiation / neuron migration / positive regulation of protein-containing complex assembly / response to toxic substance / cerebral cortex development / cellular response to virus / activation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Priyadarshi, A. / Gavathiotis, E. | ||||||
Citation | Journal: Mol.Cell / Year: 2016 Title: An Autoinhibited Dimeric Form of BAX Regulates the BAX Activation Pathway. Authors: Garner, T.P. / Reyna, D.E. / Priyadarshi, A. / Chen, H.C. / Li, S. / Wu, Y. / Ganesan, Y.T. / Malashkevich, V.N. / Almo, S.S. / Cheng, E.H. / Gavathiotis, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4s0o.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s0o.ent.gz | 118.6 KB | Display | PDB format |
PDBx/mmJSON format | 4s0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/4s0o ftp://data.pdbj.org/pub/pdb/validation_reports/s0/4s0o | HTTPS FTP |
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-Related structure data
Related structure data | 4s0pC 1f16S 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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Unit cell |
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-Components
#1: Protein | Mass: 21164.291 Da / Num. of mol.: 2 / Mutation: P168G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAX, BCL2L4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07812 #2: 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: 1.97 Å3/Da / Density % sol: 37.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 1.6 M AMMONIUM SULFATE, 0.1 M BIS-TRIS , PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2012 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 24766 / Num. obs: 24766 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.07 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.23 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F16 Resolution: 1.9→19.15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.35 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.15 Å
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