+Open data
-Basic information
Entry | Database: PDB / ID: 2voh | ||||||
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Title | Structure of mouse A1 bound to the Bak BH3-domain | ||||||
Components |
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Keywords | APOPTOSIS / BH3 / BCL-2 / MEMBRANE / PRO-SURVIVAL / TRANSMEMBRANE / PROTEIN-PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information Activation and oligomerization of BAK protein / Release of apoptotic factors from the mitochondria / leukocyte homeostasis / Pyroptosis / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration ...Activation and oligomerization of BAK protein / Release of apoptotic factors from the mitochondria / leukocyte homeostasis / Pyroptosis / response to mycotoxin / 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 / 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 / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of endoplasmic reticulum unfolded protein response / negative regulation of B cell apoptotic process / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / channel activity / mitochondrial fusion / fibroblast apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / porin activity / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / positive regulation of proteolysis / positive regulation of release of cytochrome c from mitochondria / vagina development / B cell homeostasis / homeostasis of number of cells / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / animal organ regeneration / negative regulation of peptidyl-serine phosphorylation / 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 / positive regulation of protein-containing complex assembly / mitochondrial membrane / response to gamma radiation / 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 / response to ethanol / 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 / protein-containing complex binding / negative regulation of apoptotic process / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Smits, C. / Czabotar, P.E. / Hinds, M.G. / Day, C.L. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Structural Plasticity Underpins Promiscuous Binding of the Prosurvival Protein A1. Authors: Smits, C. / Czabotar, P.E. / Hinds, M.G. / Day, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2voh.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2voh.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 2voh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/2voh ftp://data.pdbj.org/pub/pdb/validation_reports/vo/2voh | HTTPS FTP |
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-Related structure data
Related structure data | 2vofSC 2vogC 2voiC 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
#1: Protein | Mass: 17922.418 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-152 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX 6P-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PSJS 1240 / References: UniProt: Q07440 |
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#2: Protein/peptide | Mass: 2917.218 Da / Num. of mol.: 1 / Fragment: BH3-DOMAIN, RESIDUES 64-89 Source method: isolated from a genetically manipulated source Details: C-TERMINAL HOMOSERINE LACTONE DUE TO CNBR CLEAVAGE. Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET31B BAK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O08734 |
#3: Chemical | ChemComp-CIT / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % / Description: NONE |
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Crystal grow | Details: 0.1 M SODIUM CITRATE (PH 5.6), 0.3 M (NH4)2SO4, 0.6 M LI2SO4 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30.61 Å / Num. obs: 12891 / % possible obs: 97.1 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.9 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VOF Resolution: 1.9→30.61 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.387 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.16 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.81 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30.61 Å
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