+Open data
-Basic information
Entry | Database: PDB / ID: 5vwv | ||||||||||||
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Title | Bak core latch dimer in complex with Bim-BH3 - Cubic | ||||||||||||
Components |
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Keywords | APOPTOSIS / Bcl-2 Family / Activator | ||||||||||||
Function / homology | Function and homology information BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / Activation and oligomerization of BAK protein / response to mycotoxin / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / developmental pigmentation / BAK complex ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / Activation and oligomerization of BAK protein / response to mycotoxin / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / developmental pigmentation / BAK complex / BH domain binding / Activation of BIM and translocation to mitochondria / 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 / response to fungus / positive regulation of fibroblast apoptotic process / limb morphogenesis / apoptotic process involved in embryonic digit morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / ear development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / meiosis I / 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 / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / cellular response to glucocorticoid stimulus / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / mitochondrial fusion / fibroblast apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / positive regulation of calcium ion transport into cytosol / porin activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / T cell homeostasis / odontogenesis of dentin-containing tooth / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / positive regulation of proteolysis / vagina development / B cell homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / blood vessel remodeling / endomembrane system / animal organ regeneration / Pyroptosis / positive regulation of cell cycle / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / heat shock protein binding / FLT3 Signaling / response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway / cell-matrix adhesion / release of cytochrome c from mitochondria / post-embryonic development / thymus development / regulation of mitochondrial membrane potential / epithelial cell proliferation / kidney development / establishment of localization in cell / response to gamma radiation / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to UV / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / protein-folding chaperone binding / microtubule binding / spermatogenesis / regulation of apoptotic process / response to ethanol / in utero embryonic development Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å | ||||||||||||
Authors | Brouwer, J.M. / Colman, P.M. / Czabotar, P.E. | ||||||||||||
Funding support | Australia, 3items
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Citation | Journal: Mol. Cell / Year: 2017 Title: Conversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design. Authors: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / ...Authors: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / Call, M.J. / Smith, B.J. / Dewson, G. / Lessene, 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 | 5vwv.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vwv.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/5vwv ftp://data.pdbj.org/pub/pdb/validation_reports/vw/5vwv | HTTPS FTP |
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-Related structure data
Related structure data | 5vwwC 5vwxC 5vwyC 5vwzC 5vx0C 5vx1C 5vx2C 5vx3C C: citing same article (ref.) |
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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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 19037.320 Da / Num. of mol.: 1 / Fragment: UNP residues 23-186 / Mutation: C166S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16611 |
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#2: Protein/peptide | Mass: 3026.411 Da / Num. of mol.: 1 / Fragment: UNP residues 141-165 / Mutation: W147R, Y163T / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521 |
-Non-polymers , 5 types, 195 molecules
#3: Chemical | ChemComp-TFA / | ||||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-GOL / | #7: 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: 5.12 Å3/Da / Density % sol: 75.96 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop Details: 18 % glycerol, 21.6 % PEG (poly-ethylene glycol) 1500 and 0.5 % ethyl acetate |
-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: Jul 12, 2014 |
Radiation | Monochromator: ADSC QUANTUM 315r / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.897→42.032 Å / Num. obs: 37157 / % possible obs: 100 % / Redundancy: 47.8 % / Rmerge(I) obs: 0.2162 / Net I/σ(I): 24.26 |
Reflection shell | Resolution: 1.898→1.966 Å / Redundancy: 47 % / Mean I/σ(I) obs: 1.48 / Num. unique obs: 3647 / CC1/2: 0.497 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.897→42.032 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.897→42.032 Å
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Refine LS restraints |
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LS refinement shell |
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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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