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- PDB-2pon: Solution structure of the Bcl-xL/Beclin-1 complex -

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Basic information

Entry
Database: PDB / ID: 2pon
TitleSolution structure of the Bcl-xL/Beclin-1 complex
Components
  • Apoptosis regulator Bcl-XBcl-2-like protein 1
  • Beclin-1BECN1
KeywordsAPOPTOSIS INHIBITOR / Apoptosis / Autophagy / Bcl-2 family proteins / Beclin-1
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 / suppression by virus of host autophagy / protein targeting to lysosome / positive regulation of mononuclear cell proliferation / early endosome to late endosome transport / 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 / SMAD protein signal transduction / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / 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 / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / positive regulation of cardiac muscle hypertrophy / hepatocyte apoptotic process / cytoplasmic pattern recognition receptor signaling pathway / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / p38MAPK cascade / apoptotic mitochondrial changes / autophagosome maturation / germ cell development / mitophagy / autophagosome assembly / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / autophagosome / neuron development / negative regulation of reactive oxygen species metabolic process / response to vitamin E / regulation of macroautophagy / ectopic germ cell programmed cell death / cellular defense response / negative regulation of intrinsic apoptotic signaling pathway / cellular response to glucose starvation / amyloid-beta metabolic process / phosphatidylinositol 3-kinase binding / phagocytic vesicle / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of autophagy / 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 / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to lead ion / cellular response to gamma radiation / trans-Golgi network / synaptic vesicle membrane / cellular response to hydrogen peroxide / ISG15 antiviral mechanism
Similarity search - Function
Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX ...Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bcl-2-like protein 1 / Beclin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsFeng, W. / Huang, S. / Wu, H. / Zhang, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Molecular Basis of Bcl-xL's Target Recognition Versatility Revealed by the Structure of Bcl-xL in Complex with the BH3 Domain of Beclin-1.
Authors: Feng, W. / Huang, S. / Wu, H. / Zhang, M.
History
DepositionApr 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beclin-1
B: Apoptosis regulator Bcl-X


Theoretical massNumber of molelcules
Total (without water)20,3992
Polymers20,3992
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #18minimized average structure

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Components

#1: Protein/peptide Beclin-1 / BECN1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 2500.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BECN1, GT197 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q14457
#2: Protein Apoptosis regulator Bcl-X / Bcl-2-like protein 1 / Bcl-2-like 1 protein


Mass: 17897.723 Da / Num. of mol.: 1 / Fragment: deletion of 45-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q07817

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
1333D 13C-separated NOESY
144HNCO, HNCA, HN(CO)CA, HN(CA)CB and CBCA(CO)NH
1553D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM unlabelled Bcl-xL/Beclin-1 complex in 99.9% D2O; 50mM potassium phosphate99.9% D2O
21.5mM uniformly 15N labelled Bcl-xL/Beclin-1 complex in 90% H2O/10% D2O; 50mM potassium phosphate90% H2O/10% D2O
31.5mM uniformly 15N/13C labelled Bcl-xL/Beclin-1 complex in 99.9% D2O; 50mM potassium phosphate99.9% D2O
41.5mM 80% deuterated, uniformly 15N/13C labelled Bcl-xL/Beclin-1 complex in 90% H2O/10% D2O; 50mM potassium phosphate90% H2O/10% D2O
51.5mM 100% deuterated, uniformly 15N labelled Bcl-xL/Beclin-1 complex in 90% H2O/10% D2O; 50mM potassium phosphate90% H2O/10% D2O
Sample conditionsIonic strength: 50mM potassium phosphate / pH: 7.0 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, A.T.structure solution
CNS1.1Brunger, A.T.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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