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Yorodumi- PDB-5w60: Crystal structure of BAXP168G monomer cryo-protected with ethylen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w60 | ||||||
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Title | Crystal structure of BAXP168G monomer cryo-protected with ethylene glycol | ||||||
Components | Apoptosis regulator BAX | ||||||
Keywords | APOPTOSIS / BAX / inactive monomer | ||||||
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 / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / development of secondary sexual characteristics / 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 / Transcriptional regulation by RUNX2 / apoptotic process involved in mammary gland involution / 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 / channel activity / motor neuron apoptotic process / mitochondrial fusion / positive regulation of epithelial cell apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / epithelial cell apoptotic process / hypothalamus development / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / BH3 domain binding / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / germ cell development / negative regulation of mitochondrial membrane potential / positive regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / negative regulation of apoptotic signaling pathway / B cell homeostasis / 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 / blood vessel remodeling / ectopic germ cell programmed cell death / cellular response to unfolded protein / Pyroptosis / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / 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 / positive regulation of protein-containing complex assembly / response to gamma radiation / neuron migration / cerebral cortex development / response to toxic substance / cellular response to virus / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å | ||||||
Authors | Robin, A.Y. / Colman, P.M. / Czabotar, P.E. | ||||||
Citation | Journal: Structure / Year: 2018 Title: Ensemble Properties of Bax Determine Its Function. Authors: Robin, A.Y. / Iyer, S. / Birkinshaw, R.W. / Sandow, J. / Wardak, A. / Luo, C.S. / Shi, M. / Webb, A.I. / Czabotar, P.E. / Kluck, R.M. / Colman, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w60.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w60.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 5w60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/5w60 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/5w60 | HTTPS FTP |
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-Related structure data
Related structure data | 5w5xC 5w5zC 5w61C 5w62C 5w63C 4bd2S 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: 21306.316 Da / Num. of mol.: 1 / Mutation: C62S C126S P168G Source method: isolated from a genetically manipulated source Details: Two additional serine residues at C-terminus due to cloning strategy. Source: (gene. exp.) Homo sapiens (human) / Gene: BAX, BCL2L4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07812 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.68 Å3/Da / Density % sol: 26.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, TRIS |
-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 315r / Detector: CCD / Date: Sep 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.803→36.174 Å / Num. obs: 13738 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07706 / Net I/σ(I): 16.9 |
Reflection shell | Highest resolution: 1.803 Å / Rmerge(I) obs: 0.8226 / CC1/2: 0.796 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BD2 Resolution: 1.803→36.174 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.803→36.174 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: -8.0742 Å / Origin y: -0.2681 Å / Origin z: 10.3055 Å
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Refinement TLS group | Selection details: chain A |