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Yorodumi- PDB-1ysw: Solution structure of the anti-apoptotic protein Bcl-2 complexed ... -
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-Basic information
Entry | Database: PDB / ID: 1ysw | ||||||
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Title | Solution structure of the anti-apoptotic protein Bcl-2 complexed with an acyl-sulfonamide-based ligand | ||||||
Components | Apoptosis regulator Bcl-2 | ||||||
Keywords | APOPTOSIS / COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / negative regulation of osteoblast proliferation / gland morphogenesis / renal system process / regulation of cell-matrix adhesion / T cell apoptotic process / stem cell development / negative regulation of calcium ion transport into cytosol / melanocyte differentiation / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / lymphoid progenitor cell differentiation / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of T cell apoptotic process / glomerulus development / negative regulation of dendritic cell apoptotic process / oocyte development / positive regulation of multicellular organism growth / metanephros development / neuron maturation / regulation of viral genome replication / negative regulation of motor neuron apoptotic process / focal adhesion assembly / endoplasmic reticulum calcium ion homeostasis / negative regulation of ossification / negative regulation of B cell apoptotic process / response to UV-B / regulation of mitochondrial membrane permeability / response to iron ion / calcium ion transport into cytosol / channel activity / negative regulation of mitochondrial depolarization / motor neuron apoptotic process / axon regeneration / epithelial cell apoptotic process / smooth muscle cell migration / intrinsic apoptotic signaling pathway in response to oxidative stress / NFE2L2 regulating tumorigenic genes / organ growth / digestive tract morphogenesis / branching involved in ureteric bud morphogenesis / hair follicle morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / : / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / B cell lineage commitment / pore complex / positive regulation of smooth muscle cell migration / B cell proliferation / T cell homeostasis / BH3 domain binding / regulation of calcium ion transport / B cell homeostasis / negative regulation of apoptotic signaling pathway / humoral immune response / negative regulation of anoikis / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Activation of BAD and translocation to mitochondria / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / behavioral fear response / cellular response to glucose starvation / skeletal muscle fiber development / negative regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of B cell proliferation / response to glucocorticoid / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / reactive oxygen species metabolic process / negative regulation of autophagy / negative regulation of cell migration / ossification / axonogenesis / release of cytochrome c from mitochondria / post-embryonic development Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
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. ...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. | ||||||
Citation | Journal: 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 |
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Remark 999 | SEQUENCE RESIDUES 49-88 (SEQUENCE DATABASE RESIDUES 45-84) ARE NOT PRESENT DUE TO A LOOP DELETION. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ysw.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ysw.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ysw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ysw_validation.pdf.gz | 397.7 KB | Display | wwPDB validaton report |
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Full document | 1ysw_full_validation.pdf.gz | 397.6 KB | Display | |
Data in XML | 1ysw_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1ysw_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/1ysw ftp://data.pdbj.org/pub/pdb/validation_reports/ys/1ysw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-43B / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1 mM Bcl-2 U-15N,13C, 25 mM Deuterated TRIS, 1 mM deuterated dithiothreitol, 100% D2O Solvent system: 100% D2O |
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Sample conditions | Ionic strength: 25 mM / pH: 8.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
-Processing
NMR software | Name: X-PLOR / Version: 3.1 / Developer: Brunger / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 |
NMR ensemble | Conformers submitted total number: 1 |