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- PDB-2o21: Solution structure of the anti-apoptotic protein Bcl-2 in complex... -

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Basic information

Entry
Database: PDB / ID: 2o21
TitleSolution structure of the anti-apoptotic protein Bcl-2 in complex with an acyl-sulfonamide-based ligand
ComponentsApoptosis regulator Bcl-2
KeywordsAPOPTOSIS / complex / bcl
Function / homology
Function and homology information


: / channel inhibitor activity / dendritic cell apoptotic process / dendritic cell proliferation / apoptotic process in bone marrow cell / The NLRP1 inflammasome / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / negative regulation of dendritic cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members ...: / channel inhibitor activity / dendritic cell apoptotic process / dendritic cell proliferation / apoptotic process in bone marrow cell / The NLRP1 inflammasome / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / negative regulation of dendritic cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / fertilization / negative regulation of execution phase of apoptosis / pigmentation / hair follicle morphogenesis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of viral genome replication / endoplasmic reticulum calcium ion homeostasis / Regulation of MITF-M-dependent genes involved in apoptosis / regulation of growth / regulation of mitochondrial membrane permeability / germ cell development / apoptotic mitochondrial changes / response to iron ion / negative regulation of mitochondrial depolarization / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / hepatocyte apoptotic process / response to cycloheximide / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / STAT5 activation downstream of FLT3 ITD mutants / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / humoral immune response / pore complex / B cell proliferation / regulation of calcium ion transport / negative regulation of reproductive process / negative regulation of developmental process / ectopic germ cell programmed cell death / negative regulation of apoptotic signaling pathway / negative regulation of anoikis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / BH3 domain binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Activation of BAD and translocation to mitochondria / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / epithelial cell proliferation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein localization to plasma membrane / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of B cell proliferation / response to cytokine / release of cytochrome c from mitochondria / negative regulation of autophagy / regulation of mitochondrial membrane potential / protein phosphatase 2A binding / B cell receptor signaling pathway / cellular response to amino acid stimulus / regulation of cytokinesis / response to nicotine / male gonad development / female pregnancy / cellular response to gamma radiation / response to radiation / intrinsic apoptotic signaling pathway in response to DNA damage / response to toxic substance / autophagy / endocytosis / in utero embryonic development / protein polyubiquitination / RAS processing / neuron apoptotic process / myelin sheath / synaptic vesicle membrane / nuclear membrane / positive regulation of cell growth / channel activity / protease binding / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / negative regulation of neuron apoptotic process / Estrogen-dependent gene expression / DNA-binding transcription factor binding / sequence-specific DNA binding / defense response to virus / molecular adaptor activity / mitochondrial outer membrane / mitochondrial inner membrane / response to xenobiotic stimulus / positive regulation of apoptotic process / mitochondrial matrix / protein heterodimerization activity / centrosome / positive regulation of cell population proliferation / ubiquitin protein ligase binding
Similarity search - Function
Apoptosis regulator, Bcl-2 / 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-2 / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-43B / Apoptosis regulator Bcl-2 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBruncko, M. / Oost, T.K. / Belli, B.A. / Ding, H. / Joseph, M.K. / Kunzer, A. / Martineau, D. / McClellan, W.J. / Mitten, M. / Ng, S.C. ...Bruncko, M. / Oost, T.K. / Belli, B.A. / Ding, H. / Joseph, M.K. / Kunzer, A. / Martineau, D. / McClellan, W.J. / Mitten, M. / Ng, S.C. / Nimmer, P.M. / Oltersdorf, T. / Park, C.M. / Petros, A.M. / Shoemaker, A.R. / Song, X. / Wang, X. / Wendt, M.D. / Zhang, H. / Fesik, S.W. / Rosenberg, S.H. / Elmore, S.W.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Studies Leading to Potent, Dual Inhibitors of Bcl-2 and Bcl-xL.
Authors: Bruncko, M. / Oost, T.K. / Belli, B.A. / Ding, H. / Joseph, M.K. / Kunzer, A. / Martineau, D. / McClellan, W.J. / Mitten, M. / Ng, S.C. / Nimmer, P.M. / Oltersdorf, T. / Park, C.M. / Petros, ...Authors: Bruncko, M. / Oost, T.K. / Belli, B.A. / Ding, H. / Joseph, M.K. / Kunzer, A. / Martineau, D. / McClellan, W.J. / Mitten, M. / Ng, S.C. / Nimmer, P.M. / Oltersdorf, T. / Park, C.M. / Petros, A.M. / Shoemaker, A.R. / Song, X. / Wang, X. / Wendt, M.D. / Zhang, H. / Fesik, S.W. / Rosenberg, S.H. / Elmore, S.W.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8502
Polymers19,1551
Non-polymers6951
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1average-minimized

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Components

#1: Protein Apoptosis regulator Bcl-2


Mass: 19155.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P10415, UniProt: Q07817
#2: Chemical ChemComp-43B / 3-NITRO-N-{4-[2-(2-PHENYLETHYL)-1,3-BENZOTHIAZOL-5-YL]BENZOYL}-4-{[2-(PHENYLSULFANYL)ETHYL]AMINO}BENZENESULFONAMIDE


Mass: 694.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H30N4O5S3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 13C-SEPARATED NOESY

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Sample preparation

DetailsContents: 25mM TRIS buffer; 150 mM sodium chloride; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 25 mM TRIS; 150 mM sodium chloride / pH: 8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. etall / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: average-minimized
NMR ensembleConformers submitted total number: 1

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