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Open data
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Basic information
Entry | Database: PDB / ID: 3ilb | ||||||
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Title | Crystal structure of mouse Bcl-xl mutant (R139A) at pH 6.0 | ||||||
![]() | Bcl-2-like protein 1 | ||||||
![]() | APOPTOSIS / BH3 domain / Bcl-2 / Membrane / Mitochondrion / Transmembrane | ||||||
Function / homology | ![]() The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of synaptic vesicle endocytosis ...The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of synaptic vesicle endocytosis / positive regulation of mononuclear cell proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of mitochondrial membrane permeability / regulation of growth / negative regulation of protein localization to plasma membrane / Bcl-2 family protein complex / BH domain binding / response to cycloheximide / clathrin binding / regulation of long-term synaptic depression / positive regulation of ATP biosynthetic process / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / BH3 domain binding / germ cell development / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / ectopic germ cell programmed cell death / 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 / MDM2/MDM4 family protein binding / release of cytochrome c from mitochondria / regulation of cytokinesis / regulation of mitochondrial membrane potential / mitochondrion organization / epithelial cell proliferation / response to cytokine / response to ischemia / mitochondrial membrane / cellular response to amino acid stimulus / response to virus / response to radiation / cellular response to gamma radiation / synaptic vesicle membrane / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / GTPase binding / presynapse / spermatogenesis / nuclear membrane / neuron apoptotic process / regulation of apoptotic process / defense response to virus / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / centrosome / protein-containing complex binding / negative regulation of apoptotic process / apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Priyadarshi, A. / Hwang, K.Y. | ||||||
![]() | ![]() Title: Structural insights into mouse anti-apoptotic Bcl-xl reveal affinity for Beclin 1 and gossypol. Authors: Priyadarshi, A. / Roy, A. / Kim, K.S. / Kim, E.E. / Hwang, K.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.4 KB | Display | ![]() |
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PDB format | ![]() | 53.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ihcC ![]() 3ihdC ![]() 3iheC ![]() 3ihfC ![]() 3iigC ![]() 3iihC ![]() 3ilcC ![]() 1pq0S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21970.094 Da / Num. of mol.: 2 / Fragment: UNP residues 1-196 / Mutation: R139A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.2M Ammonium sulphate, 0.3M Lithium sulphate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 8, 2008 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. all: 13028 / Num. obs: 12366 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.34 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2.38→2.47 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1274 / Rsym value: 0.34 / % possible all: 91.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PQ0 Resolution: 2.38→35.45 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.859 / SU B: 8.525 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.563 / ESU R Free: 0.324 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.912 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→35.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.377→2.439 Å / Total num. of bins used: 20
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