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- PDB-2m03: Solution structure of BCL-xL determined with selective isotope la... -
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Basic information
Entry | Database: PDB / ID: 2m03 | ||||||
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Title | Solution structure of BCL-xL determined with selective isotope labelling of I,L,V sidechains | ||||||
![]() | Bcl-2-like protein 1 | ||||||
![]() | APOPTOSIS / BCL-xL / PUMA | ||||||
Function / homology | ![]() 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 / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of cytokinesis / regulation of mitochondrial membrane potential / epithelial cell proliferation / response to cytokine / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / RAS processing / endocytosis / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / nuclear membrane / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / torsion angle simulated annealing, molecular dynamics | ||||||
![]() | Viacava Follis, A. / Royappa, G. / Kriwacki, R.W. | ||||||
![]() | ![]() Title: PUMA binding induces partial unfolding within BCL-xL to disrupt p53 binding and promote apoptosis. Authors: Follis, A.V. / Chipuk, J.E. / Fisher, J.C. / Yun, M.K. / Grace, C.R. / Nourse, A. / Baran, K. / Ou, L. / Min, L. / White, S.W. / Green, D.R. / Kriwacki, R.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 908.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 20804.918 Da / Num. of mol.: 1 / Mutation: delta(45-84) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 0.9 mM [U-100% 13C; U-100% 15N; U-95% 2H; Ile,Leu,Val C1H3] BCL-xL, 92% H2O/8% D2O Solvent system: 92% H2O/8% D2O |
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Sample | Conc.: 0.9 mM / Component: BCL-xL-1 Isotopic labeling: [U-100% 13C; U-100% 15N; U-95% 2H; Ile,Leu,Val C1H3] |
Sample conditions | Ionic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 298.1 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: torsion angle simulated annealing, molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 524 / NOE intraresidue total count: 40 / NOE long range total count: 109 / NOE medium range total count: 186 / NOE sequential total count: 189 / Hydrogen bond constraints total count: 140 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 115 / Protein psi angle constraints total count: 114 | ||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.57 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 4.66 ° / Maximum upper distance constraint violation: 0.29 Å / Torsion angle constraint violation method: CYANA run output | ||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.017 Å / Distance rms dev error: 0.002 Å |