+Open data
-Basic information
Entry | Database: PDB / ID: 3ilc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of mouse Bcl-xl mutant (Y101A) at pH 6.0 | ||||||
Components | Bcl-2-like protein 1 | ||||||
Keywords | APOPTOSIS / BH3 domain / Bcl-2 / Alternative splicing / Cytoplasm / Membrane / Mitochondrion / Transmembrane | ||||||
Function / homology | Function and homology information 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Priyadarshi, A. / Hwang, K.Y. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2010 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ilc.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ilc.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ilc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ilc_validation.pdf.gz | 429 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ilc_full_validation.pdf.gz | 431.2 KB | Display | |
Data in XML | 3ilc_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 3ilc_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/3ilc ftp://data.pdbj.org/pub/pdb/validation_reports/il/3ilc | HTTPS FTP |
-Related structure data
Related structure data | 3ihcC 3ihdC 3iheC 3ihfC 3iigC 3iihC 3ilbC 1pq0S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22102.260 Da / Num. of mol.: 1 / Fragment: UNP residues 1-196 / Mutation: Y101A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcl-xl, Bcl2l, Bcl2l1, Bclx / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q64373 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.08 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.6M Ammonium sulphate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 27, 2009 / 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: 1.64→50 Å / Num. all: 26338 / Num. obs: 24986 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.33 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1758 / Rsym value: 0.33 / % possible all: 64.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PQ0 Resolution: 1.64→44.45 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.177 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.088 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 31.323 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→44.45 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.64→1.682 Å / Total num. of bins used: 20
|