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Yorodumi- PDB-4zie: Crystal Structure of core/latch dimer of Bax in complex with BimBH3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zie | |||||||||||||||
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Title | Crystal Structure of core/latch dimer of Bax in complex with BimBH3 | |||||||||||||||
Components |
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Keywords | APOPTOSIS / Bax / BH3 domain / Structural Genomics | |||||||||||||||
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 / BIM-BCL-xl complex / BIM-BCL-2 complex ...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 / BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / 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 / RUNX3 regulates BCL2L11 (BIM) transcription / 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 / developmental pigmentation / BAK complex / Activation of BIM and translocation to mitochondria / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / mitochondrial fragmentation involved in apoptotic process / positive regulation of fibroblast apoptotic process / 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 / ear development / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / Transcriptional regulation by RUNX2 / meiosis I / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / cellular response to glucocorticoid stimulus / positive regulation of epithelial cell apoptotic process / calcium ion transport into cytosol / channel activity / motor neuron apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / positive regulation of calcium ion transport into cytosol / hypothalamus development / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / pore complex / thymocyte apoptotic process / BH3 domain binding / T cell homeostasis / germ cell development / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / negative regulation of mitochondrial membrane potential / positive regulation of release of cytochrome c from mitochondria / 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 / endomembrane system / Pyroptosis / positive regulation of cell cycle / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / ovarian follicle development / release of sequestered calcium ion into cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.797 Å | |||||||||||||||
Authors | Krishna Kumar, K. / Robin, A.Y. / Westphal, D. / Wardak, A.Z. / Thompson, G.V. / Dewson, G. / Colman, P.M. / Czabotar, P.E. | |||||||||||||||
Funding support | Australia, 4items
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Citation | Journal: Cell Death Dis / Year: 2015 Title: Crystal structure of Bax bound to the BH3 peptide of Bim identifies important contacts for interaction. Authors: Robin, A.Y. / Krishna Kumar, K. / Westphal, D. / Wardak, A.Z. / Thompson, G.V. / Dewson, G. / Colman, P.M. / Czabotar, P.E. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zie.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zie.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 4zie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zie_validation.pdf.gz | 445 KB | Display | wwPDB validaton report |
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Full document | 4zie_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 4zie_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 4zie_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/4zie ftp://data.pdbj.org/pub/pdb/validation_reports/zi/4zie | HTTPS FTP |
-Related structure data
Related structure data | 4zifC 4zigC 4zihC 4ziiC 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: 18511.996 Da / Num. of mol.: 1 / Mutation: C62S C126S 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 |
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#2: Protein/peptide | Mass: 3274.691 Da / Num. of mol.: 1 / Fragment: BH3 motif, UNP RESIDUES 141-166 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521 |
#3: Chemical | ChemComp-EDO / |
#4: 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: 1.9 Å3/Da / Density % sol: 35.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: PEG6000, bicine |
-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: Aug 22, 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: 1.797→33.97 Å / Num. obs: 16194 / % possible obs: 99.92 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.0639 / Net I/σ(I): 30.73 |
Reflection shell | Resolution: 1.797→1.861 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.184 / Mean I/σ(I) obs: 2.57 / % possible all: 99.43 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BD2 Resolution: 1.797→33.97 Å / FOM work R set: 0.8487 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.61 Å2 / Biso mean: 38.28 Å2 / Biso min: 13.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.797→33.97 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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