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Open data
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Basic information
Entry | Database: PDB / ID: 3iig | ||||||
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Title | Crystal structure of mouse Bcl-xl mutant (F105A) at pH 5.0 | ||||||
![]() | Bcl-2-like protein 1 | ||||||
![]() | APOPTOSIS / BH3 domain / Bcl-2 / Membrane / Mitochondrion / Transmembrane | ||||||
Function / homology | ![]() The NLRP1 inflammasome / synaptic vesicle recycling via endosome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / BH domain binding / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation ...The NLRP1 inflammasome / synaptic vesicle recycling via endosome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / BH domain binding / 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 / negative regulation of protein localization to plasma membrane / regulation of growth / Bcl-2 family protein complex / regulation of long-term synaptic depression / response to cycloheximide / clathrin binding / positive regulation of ATP biosynthetic process / cellular response to alkaloid / 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 / 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 intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / MDM2/MDM4 family protein binding / extrinsic apoptotic signaling pathway in absence of ligand / mitochondrion organization / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / 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 / presynapse / GTPase binding / spermatogenesis / regulation of apoptotic process / nuclear membrane / neuron apoptotic process / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / protein heterodimerization activity / centrosome / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.1 KB | Display | ![]() |
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PDB format | ![]() | 29 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.9 KB | Display | ![]() |
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Full document | ![]() | 431.7 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 10.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ihcC ![]() 3ihdC ![]() 3iheC ![]() 3ihfC ![]() 3iihC ![]() 3ilbC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 21980.113 Da / Num. of mol.: 1 / Fragment: UNP residues 1-196 / Mutation: F105A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.86 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.6M Ammonium sulphate, 0.1M tri-Na citrate, pH 5.0, 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: 2.3→40 Å / Num. all: 9693 / Num. obs: 9215 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.24 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 3.1 / Num. unique all: 772 / Rsym value: 0.24 / % possible all: 76.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PQ0 Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.739 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.283 / ESU R Free: 0.228 / 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: 48.869 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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