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Open data
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Basic information
Entry | Database: PDB / ID: 2p1l | ||||||
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Title | Structure of the Bcl-XL:Beclin 1 complex | ||||||
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![]() | APOPTOSIS / autophagy / beclin / BH3 domain / Bcl | ||||||
Function / homology | ![]() cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization ...cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / positive regulation of stress granule assembly / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / apoptotic process in bone marrow cell / positive regulation of autophagosome assembly / negative regulation of autophagosome assembly / receptor catabolic process / SARS-CoV-1-mediated effects on programmed cell death / engulfment of apoptotic cell / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / suppression by virus of host autophagy / protein targeting to lysosome / early endosome to late endosome transport / late endosome to vacuole transport / cellular response to nitrogen starvation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / SMAD protein signal transduction / 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 / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / negative regulation of programmed cell death / response to iron(II) ion / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / Bcl-2 family protein complex / phosphatidylinositol-3-phosphate biosynthetic process / NFE2L2 regulating tumorigenic genes / mitotic metaphase chromosome alignment / response to cycloheximide / cytoplasmic pattern recognition receptor signaling pathway / Macroautophagy / RSV-host interactions / lysosome organization / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / positive regulation of cardiac muscle hypertrophy / 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 / p38MAPK cascade / germ cell development / apoptotic mitochondrial changes / mitophagy / autophagosome maturation / negative regulation of anoikis / autophagosome assembly / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of reactive oxygen species metabolic process / neuron development / autophagosome / response to vitamin E / ectopic germ cell programmed cell death / regulation of macroautophagy / amyloid-beta metabolic process / cellular defense response / cellular response to glucose starvation / positive regulation of autophagy / phosphatidylinositol 3-kinase binding / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / JNK cascade / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / phagocytic vesicle / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / regulation of autophagy / response to cytokine / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to amino acid stimulus / response to lead ion / trans-Golgi network / cellular response to gamma radiation / ISG15 antiviral mechanism Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeffrey, P.D. / Shi, Y. / Oberstein, A.L. | ||||||
![]() | ![]() Title: Crystal structure of the Bcl-XL-Beclin 1 peptide complex: Beclin 1 is a novel BH3-only protein Authors: Oberstein, A. / Jeffrey, P.D. / Shi, 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 | ![]() | 138.8 KB | Display | ![]() |
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PDB format | ![]() | 111 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486 KB | Display | ![]() |
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Full document | ![]() | 500.3 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Details | Unique heterodimeric complex is formed between chains A and B, (Bcl-XL and Beclin 1 respectively). A dimer of heterodimers is formed between the A+B and C+D complexes via a domain-swapped helix. There are two of these "dimers of heterodimers" in the asymmetric unit. |
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Components
#1: Protein | Mass: 17506.504 Da / Num. of mol.: 4 / Fragment: Bcl-XL Delta-loop / Mutation: Loop 27-82 deletion mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 3381.751 Da / Num. of mol.: 4 / Fragment: Beclin 1 / Mutation: BH3 domain (residues 107-135) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 24% (w/v) PEG-400, 0.1M HEPES pH7.5, 0.2M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2006 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 46829 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.99 % / Biso Wilson estimate: 54.1 Å2 / Rsym value: 0.071 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 4664 / Rsym value: 0.413 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.97 Å2 / ksol: 0.337809 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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