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Yorodumi- PDB-1ysi: Solution structure of the anti-apoptotic protein Bcl-xL in comple... -
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-Basic information
Entry | Database: PDB / ID: 1ysi | |||||||||
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Title | Solution structure of the anti-apoptotic protein Bcl-xL in complex with an acyl-sulfonamide-based ligand | |||||||||
Components | Apoptosis regulator Bcl-X | |||||||||
Keywords | APOPTOSIS / COMPLEX | |||||||||
Function / homology | Function and homology information apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / 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 execution phase of apoptosis / negative regulation of dendritic cell apoptotic process ...apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / 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 execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of mitochondrial membrane permeability / regulation of growth / negative regulation of protein localization to plasma membrane / Bcl-2 family protein complex / BH domain binding / NFE2L2 regulating tumorigenic genes / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / epithelial cell proliferation / negative regulation of autophagy / cellular response to amino acid stimulus / release of cytochrome c from mitochondria / regulation of cytokinesis / regulation of mitochondrial membrane potential / response to cytokine / cellular response to gamma radiation / synaptic vesicle membrane / RAS processing / endocytosis / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / nuclear membrane / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / defense response to virus / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / cytoplasm / cytosol 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 | 1ysi.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ysi.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ysi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/1ysi ftp://data.pdbj.org/pub/pdb/validation_reports/ys/1ysi | HTTPS FTP |
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-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: 20804.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pET30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07817 |
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#2: Chemical | ChemComp-N3B / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1mM Bcl-xL U-15N,13C 50mM sodium phosphate, 5 mM deuterated Dithiothreitol, 100% D2O Solvent system: 100% D2O |
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Sample conditions | Ionic strength: 50 mM / pH: 7 / Pressure: ambient / Temperature: 303 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 |