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- PDB-1ysw: Solution structure of the anti-apoptotic protein Bcl-2 complexed ... -

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Entry
Database: PDB / ID: 1ysw
TitleSolution structure of the anti-apoptotic protein Bcl-2 complexed with an acyl-sulfonamide-based ligand
ComponentsApoptosis regulator Bcl-2
KeywordsAPOPTOSIS / COMPLEX
Function / homology
Function and homology information


BCL-2 complex / BAD-BCL-2 complex / channel inhibitor activity / The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / hair follicle morphogenesis / regulation of viral genome replication / pigmentation / endoplasmic reticulum calcium ion homeostasis / Regulation of MITF-M-dependent genes involved in apoptosis ...BCL-2 complex / BAD-BCL-2 complex / channel inhibitor activity / The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / hair follicle morphogenesis / regulation of viral genome replication / pigmentation / endoplasmic reticulum calcium ion homeostasis / Regulation of MITF-M-dependent genes involved in apoptosis / regulation of mitochondrial membrane permeability / B cell proliferation / response to iron ion / negative regulation of mitochondrial depolarization / NFE2L2 regulating tumorigenic genes / pore complex / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of intrinsic apoptotic signaling pathway / humoral immune response / regulation of calcium ion transport / negative regulation of apoptotic signaling pathway / negative regulation of anoikis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway in absence of ligand / BH3 domain binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of B cell proliferation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / neuron apoptotic process / release of cytochrome c from mitochondria / response to cytokine / B cell receptor signaling pathway / regulation of mitochondrial membrane potential / negative regulation of autophagy / protein phosphatase 2A binding / response to nicotine / intrinsic apoptotic signaling pathway in response to DNA damage / female pregnancy / myelin sheath / response to radiation / response to toxic substance / protein polyubiquitination / positive regulation of cell growth / negative regulation of neuron apoptotic process / nuclear membrane / defense response to virus / channel activity / protease binding / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / Estrogen-dependent gene expression / sequence-specific DNA binding / molecular adaptor activity / mitochondrial outer membrane / response to xenobiotic stimulus / positive regulation of apoptotic process / apoptotic process / protein heterodimerization activity / ubiquitin protein ligase binding / positive regulation of cell population proliferation / DNA damage response / negative regulation of apoptotic process / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Bcl-2 / 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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsOltersdorf, T. / Elmore, S.W. / Shoemaker, A.R. / Armstrong, R.C. / Augeri, D.J. / Belli, B.A. / Bruncko, M. / Deckwerth, T.L. / Dinges, J. / Hajduk, P.J. ...Oltersdorf, T. / Elmore, S.W. / Shoemaker, A.R. / Armstrong, R.C. / Augeri, D.J. / Belli, B.A. / Bruncko, M. / Deckwerth, T.L. / Dinges, J. / Hajduk, P.J. / Joseph, M.K. / Kitada, S. / Korsmeyer, S.J. / Kunzer, A.R. / Letai, A. / Li, C. / Mitten, M.J. / Nettesheim, D.G. / Ng, S. / Nimmer, P.M. / O'Connor, J.M. / Oleksijew, A. / Petros, A.M. / Reed, J.C. / Shen, W. / Tahir, S.K. / Thompson, C.B. / Tomaselli, K.J. / Wang, B. / Wendt, M.D. / Zhang, H. / Fesik, S.W. / Rosenberg, S.H.
CitationJournal: Nature / Year: 2005
Title: An inhibitor of Bcl-2 family proteins induces regression of solid tumours
Authors: Oltersdorf, T. / Elmore, S.W. / Shoemaker, A.R. / Armstrong, R.C. / Augeri, D.J. / Belli, B.A. / Bruncko, M. / Deckwerth, T.L. / Dinges, J. / Hajduk, P.J. / Joseph, M.K. / Kitada, S. / ...Authors: Oltersdorf, T. / Elmore, S.W. / Shoemaker, A.R. / Armstrong, R.C. / Augeri, D.J. / Belli, B.A. / Bruncko, M. / Deckwerth, T.L. / Dinges, J. / Hajduk, P.J. / Joseph, M.K. / Kitada, S. / Korsmeyer, S.J. / Kunzer, A.R. / Letai, A. / Li, C. / Mitten, M.J. / Nettesheim, D.G. / Ng, S. / Nimmer, P.M. / O'Connor, J.M. / Oleksijew, A. / Petros, A.M. / Reed, J.C. / Shen, W. / Tahir, S.K. / Thompson, C.B. / Tomaselli, K.J. / Wang, B. / Wendt, M.D. / Zhang, H. / Fesik, S.W. / Rosenberg, S.H.
History
DepositionFeb 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE RESIDUES 49-88 (SEQUENCE DATABASE RESIDUES 45-84) ARE NOT PRESENT DUE TO A LOOP DELETION.

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Structure visualization

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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 / -
Representative

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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
#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 experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 13C-edited 12C-filtered NOESY

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Sample preparation

DetailsContents: 1 mM Bcl-2 U-15N,13C, 25 mM Deuterated TRIS, 1 mM deuterated dithiothreitol, 100% D2O
Solvent system: 100% D2O
Sample conditionsIonic strength: 25 mM / pH: 8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.1 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformers submitted total number: 1

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