+Open data
-Basic information
Entry | Database: PDB / ID: 7m5a | ||||||
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Title | Crystal Structure of human BAK in complex with W3W5_BID | ||||||
Components |
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Keywords | APOPTOSIS / protein-peptide complex | ||||||
Function / homology | Function and homology information cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / response to mycotoxin / Activation, myristolyation of BID and translocation to mitochondria / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis ...cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / response to mycotoxin / Activation, myristolyation of BID and translocation to mitochondria / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / positive regulation of fibroblast apoptotic process / Release of apoptotic factors from the mitochondria / limb morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / B cell apoptotic process / protein targeting to mitochondrion / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / regulation of epithelial cell proliferation / establishment of protein localization to membrane / endoplasmic reticulum calcium ion homeostasis / death receptor binding / positive regulation of endoplasmic reticulum unfolded protein response / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of mitochondrial membrane potential / 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 / mitochondrial ATP synthesis coupled electron transport / positive regulation of calcium ion transport into cytosol / porin activity / regulation of T cell proliferation / thymocyte apoptotic process / hepatocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / regulation of G1/S transition of mitotic cell cycle / positive regulation of proteolysis / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / B cell homeostasis / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Activation of BAD and translocation to mitochondria / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / animal organ regeneration / supramolecular fiber organization / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / signal transduction in response to DNA damage / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / apoptotic signaling pathway / response to gamma radiation / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / protein-folding chaperone binding / protein-containing complex assembly / response to ethanol / neuron apoptotic process / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Singh, G. / Aggarwal, A. / Moldoveanu, T. | ||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis of BAK activation in mitochondrial apoptosis initiation. Authors: Singh, G. / Guibao, C.D. / Seetharaman, J. / Aggarwal, A. / Grace, C.R. / McNamara, D.E. / Vaithiyalingam, S. / Waddell, M.B. / Moldoveanu, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m5a.cif.gz | 54.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m5a.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 7m5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/7m5a ftp://data.pdbj.org/pub/pdb/validation_reports/m5/7m5a | HTTPS FTP |
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-Related structure data
Related structure data | 7m5bC 7m5cC 2vwzS S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18714.982 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Plasmid: pNIC28Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 placI/Y / References: UniProt: Q16611 |
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#2: Protein/peptide | Mass: 2673.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P55957 |
#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: 2.03 Å3/Da / Density % sol: 39.43 % / Mosaicity: 0.329 ° |
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Crystal grow | Temperature: 293 K / Method: evaporation / Details: 0.2 M Potassium Sodium tartrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 4, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 26921 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.49 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.019 / Rrim(I) all: 0.052 / Χ2: 1.058 / Net I/σ(I): 13.5 / Num. measured all: 185563 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2vwz Resolution: 1.5→35.697 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.41 / 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: 70.57 Å2 / Biso mean: 22.1179 Å2 / Biso min: 8.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→35.697 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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