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Yorodumi- PDB-3r85: Crystal structure of human SOUL BH3 domain in complex with Bcl-xL -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r85 | ||||||
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Title | Crystal structure of human SOUL BH3 domain in complex with Bcl-xL | ||||||
Components |
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Keywords | APOPTOSIS / Bcl-2-like protein / Inhibitor of cell death / SOUL protein | ||||||
Function / homology | Function and homology information apoptotic process in bone marrow cell / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis ...apoptotic process in bone marrow cell / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / negative regulation of protein localization to plasma membrane / regulation of mitochondrial membrane permeability / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / apoptotic mitochondrial changes / germ cell development / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / azurophil granule lumen / spermatogenesis / defense response to virus / neuron apoptotic process / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / in utero embryonic development / mitochondrial inner membrane / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Ambrosi, E.K. / Capaldi, S. / Bovi, M. / Saccomani, G. / Perduca, M. / Monaco, H.L. | ||||||
Citation | Journal: Biochem.J. / Year: 2011 Title: Structural changes in the BH3 domain of SOUL protein upon interaction with the anti-apoptotic protein Bcl-xL. Authors: Ambrosi, E. / Capaldi, S. / Bovi, M. / Saccomani, G. / Perduca, M. / Monaco, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r85.cif.gz | 258.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r85.ent.gz | 210.1 KB | Display | PDB format |
PDBx/mmJSON format | 3r85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/3r85 ftp://data.pdbj.org/pub/pdb/validation_reports/r8/3r85 | HTTPS FTP |
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-Related structure data
Related structure data | 3r8jC 3r8kC 2yxjS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 17788.781 Da / Num. of mol.: 4 Fragment: residues 1-209 with the deletion of residues 27-82 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q07817 #2: Protein/peptide | Mass: 2965.315 Da / Num. of mol.: 4 / Fragment: residues 147 to 172 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y5Z4 #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M sodium sulphate, 15% PEG 6000, 0.3M 1-butyl-3-methylimidazolium 2-(2-methoxyethoxy)ethyl sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9769 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2010 |
Radiation | Monochromator: liquid-nitrogen-cooled channel-cut silicon [111] monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9769 Å / Relative weight: 1 |
Reflection twin | Type: merohedral / Operator: h,-k,-l / Fraction: 0.503 |
Reflection | Resolution: 1.95→53.1 Å / Num. all: 54709 / Num. obs: 54709 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 6 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YXJ Resolution: 1.95→36.737 Å / Cross valid method: THROUGHOUT / σ(F): 1.44 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.97 Å2 / ksol: 0.421 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.95→36.737 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 30.6976 Å / Origin y: 36.4093 Å / Origin z: 96.1212 Å
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Refinement TLS group | Selection details: all |