+Open data
-Basic information
Entry | Database: PDB / ID: 2voi | ||||||
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Title | Structure of mouse A1 bound to the Bid BH3-domain | ||||||
Components |
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Keywords | APOPTOSIS / PROTEIN-PROTEIN COMPLEX / BH3 / BCL-2 / MEMBRANE / PRO-SURVIVAL / MITOCHONDRION / PHOSPHOPROTEIN | ||||||
Function / homology | Function and homology information Activation, myristolyation of BID and translocation to mitochondria / positive regulation of autophagy in response to ER overload / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation of BAD and translocation to mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / mitochondrial outer membrane permeabilization / BH domain binding / positive regulation of fibroblast apoptotic process / B cell apoptotic process ...Activation, myristolyation of BID and translocation to mitochondria / positive regulation of autophagy in response to ER overload / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation of BAD and translocation to mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / mitochondrial outer membrane permeabilization / BH domain binding / positive regulation of fibroblast apoptotic process / B cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein targeting to mitochondrion / regulation of epithelial cell proliferation / establishment of protein localization to membrane / negative regulation of B cell apoptotic process / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of mitochondrial membrane potential / channel activity / regulation of mitochondrial membrane permeability involved in apoptotic process / mitochondrial fusion / mitochondrial ATP synthesis coupled electron transport / regulation of T cell proliferation / hepatocyte apoptotic process / apoptotic mitochondrial changes / regulation of G1/S transition of mitotic cell cycle / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / supramolecular fiber organization / positive regulation of intrinsic apoptotic signaling pathway / signal transduction in response to DNA damage / positive regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / mitochondrial membrane / intrinsic apoptotic signaling pathway in response to DNA damage / protein-containing complex assembly / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / mitochondrion / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 2voi.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2voi.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 2voi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/2voi ftp://data.pdbj.org/pub/pdb/validation_reports/vo/2voi | HTTPS FTP |
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-Related structure data
Related structure data | 2vofSC 2vogC 2vohC 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: 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: 3941.365 Da / Num. of mol.: 1 / Fragment: BH3-DOMAIN, RESIDUES 76-109 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P70444 |
#3: Chemical | ChemComp-CL / |
#4: 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: 1.84 Å3/Da / Density % sol: 33 % / Description: NONE |
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Crystal grow | Details: 0.1 M CITRIC ACID, KOH (PH 4.2), 18% PEG 2000, 0.4 M LICL |
-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: 2.1→28.54 Å / Num. obs: 9930 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VOF Resolution: 2.1→26.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 13.326 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.2 / 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: 52.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→26.94 Å
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