+Open data
-Basic information
Entry | Database: PDB / ID: 3ihd | ||||||
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Title | Crystal structure of mouse Bcl-xl mutant (Y101A) at pH 5.0 | ||||||
Components | Bcl-2-like protein 1 | ||||||
Keywords | APOPTOSIS / BH3 domain / Bcl-2 / Membrane / Mitochondrion / Transmembrane | ||||||
Function / homology | Function and homology information 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ihd.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ihd.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 3ihd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/3ihd ftp://data.pdbj.org/pub/pdb/validation_reports/ih/3ihd | HTTPS FTP |
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-Related structure data
Related structure data | 3ihcC 3iheC 3ihfC 3iigC 3iihC 3ilbC 3ilcC 1pq0S 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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Unit cell |
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-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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 1.4M Ammonium Sulphate, 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: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å |
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: 1.88→50 Å / Num. all: 17580 / Num. obs: 16650 / % possible obs: 93.45 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.34 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.88→1.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 1.6 / Num. unique all: 949 / Rsym value: 0.34 / % possible all: 51.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PQ0 Resolution: 1.88→41.24 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.611 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.112 / ESU R Free: 0.115 / 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: 20.758 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→41.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.881→1.93 Å / Total num. of bins used: 20
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