+Open data
-Basic information
Entry | Database: PDB / ID: 2p1l | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the Bcl-XL:Beclin 1 complex | ||||||
Components |
| ||||||
Keywords | APOPTOSIS / autophagy / beclin / BH3 domain / Bcl | ||||||
Function / homology | Function and homology information cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / 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 / positive regulation of autophagosome assembly ...cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / 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 / positive regulation of autophagosome assembly / engulfment of apoptotic cell / apoptotic process in bone marrow cell / negative regulation of autophagosome assembly / receptor catabolic process / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / dendritic cell proliferation / protein targeting to lysosome / suppression by virus of host autophagy / early endosome to late endosome transport / positive regulation of mononuclear cell proliferation / cellular response to nitrogen starvation / late endosome to vacuole transport / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / SMAD protein signal transduction / phagophore assembly site / fertilization / Translation of Replicase and Assembly of the Replication Transcription Complex / response to iron(II) ion / negative regulation of programmed cell death / negative regulation of protein localization to plasma membrane / regulation of mitochondrial membrane permeability / regulation of growth / Bcl-2 family protein complex / phosphatidylinositol-3-phosphate biosynthetic process / NFE2L2 regulating tumorigenic genes / Macroautophagy / response to cycloheximide / mitotic metaphase chromosome alignment / lysosome organization / cytoplasmic pattern recognition receptor signaling pathway / 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 / apoptotic mitochondrial changes / p38MAPK cascade / germ cell development / autophagosome maturation / mitophagy / autophagosome assembly / negative regulation of anoikis / neuron development / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / autophagosome / negative regulation of reactive oxygen species metabolic process / regulation of macroautophagy / response to vitamin E / ectopic germ cell programmed cell death / cellular response to glucose starvation / negative regulation of intrinsic apoptotic signaling pathway / cellular defense response / amyloid-beta metabolic process / phosphatidylinositol 3-kinase binding / phagocytic vesicle / positive regulation of autophagy / negative regulation of endoplasmic reticulum stress-induced 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 / 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 / cellular response to amino acid stimulus / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / response to lead ion / cellular response to gamma radiation / trans-Golgi network / synaptic vesicle membrane / ISG15 antiviral mechanism / cellular response to hydrogen peroxide Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Jeffrey, P.D. / Shi, Y. / Oberstein, A.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2p1l.cif.gz | 138.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2p1l.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 2p1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/2p1l ftp://data.pdbj.org/pub/pdb/validation_reports/p1/2p1l | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
7 |
| ||||||||
Unit cell |
| ||||||||
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. |
-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.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pRSF / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q07817 #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.) Homo sapiens (human) / Gene: BECN1, GT197 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q14457 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.74 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.73 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1611649.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| |||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.97 Å2 / ksol: 0.337809 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.4 Å2
| |||||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.73 Å
| |||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| |||||||||||||||||||||||||||
Xplor file |
|