+Open data
-Basic information
Entry | Database: PDB / ID: 1pq0 | ||||||
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Title | Crystal structure of mouse Bcl-xl | ||||||
Components | Apoptosis regulator Bcl-X | ||||||
Keywords | APOPTOSIS / bcl-xl | ||||||
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: 2.2 Å | ||||||
Authors | Liu, X. / Dai, S. / Zhu, Y. / Marrack, P. / Kappler, J.W. | ||||||
Citation | Journal: Immunity / Year: 2003 Title: The structure of a Bcl-xl/Bim fragment complex: Implications for Bim function Authors: Liu, X. / Dai, S. / Zhu, Y. / Marrack, P. / Kappler, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pq0.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pq0.ent.gz | 30.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/1pq0 ftp://data.pdbj.org/pub/pdb/validation_reports/pq/1pq0 | HTTPS FTP |
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-Related structure data
Related structure data | 1pq1C 1af3S 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: 22056.209 Da / Num. of mol.: 1 / Fragment: Bcl-xl Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: BCL2L1 OR BCL2L OR BCLX / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): HI FIVE / 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: 2.51 Å3/Da / Density % sol: 51.04 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: NH4SO4, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2001 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 11386 / Num. obs: 11386 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.087 |
Reflection shell | Resolution: 2.2→2.34 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 9.4 / Num. unique all: 11386 / % possible all: 95.7 |
Reflection | *PLUS Highest resolution: 2.2 Å / Redundancy: 4.1 % |
Reflection shell | *PLUS Highest resolution: 2.2 Å / % possible obs: 88.4 % / Redundancy: 3.5 % / Num. unique obs: 968 / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AF3, Rat Bcl-xl Resolution: 2.2→19.79 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.097 Å2 / ksol: 0.372118 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.27 / Num. reflection obs: 864 |