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- PDB-2me9: Solution structure of BCL-xL containing the alpha1-alpha2 disorde... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2me9 | ||||||
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Title | Solution structure of BCL-xL containing the alpha1-alpha2 disordered loop determined with selective isotope labelling of I,L,V sidechains | ||||||
![]() | Bcl-2-like protein 1 | ||||||
![]() | APOPTOSIS / BCL-xL / p53 / BCL-2 family / cytoplasmic p53 / selective labeling | ||||||
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 / negative regulation of protein localization to plasma membrane / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / 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 mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / 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 / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
![]() | Viacava Follis, A. / Grace, C.R. / Kriwacki, R.W. | ||||||
![]() | ![]() Title: The DNA-binding domain mediates both nuclear and cytosolic functions of p53. Authors: Follis, A.V. / Llambi, F. / Ou, L. / Baran, K. / 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 | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 477.8 KB | Display | ![]() |
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Full document | ![]() | 950.3 KB | Display | |
Data in XML | ![]() | 142.3 KB | Display | |
Data in CIF | ![]() | 145 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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: 23669.945 Da / Num. of mol.: 1 / Fragment: UNP residues 1-209 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: 0.6 mM [U- 98% 13C; U- 98% 15N; U- 98% 2H; U- I,LV CH3 1H] BCL-xL, 93% H2O/7% D2O Solvent system: 93% H2O/7% D2O |
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Sample | Conc.: 0.6 mM / Component: BCL-xL-1 Isotopic labeling: [U- 98% 13C; U- 98% 15N; U- 98% 2H; U- I,LV CH3 1H] |
Sample conditions | Ionic strength: 0.05 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 Details: ENERGY MINIMIZATION WITH 100 STEPS STEEPEST GRADIENT DESCENT FOLLOWED BY 100 CONJUGATE GRADIENT DESCENT STEPS | ||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 607 / NOE intraresidue total count: 59 / NOE long range total count: 159 / NOE medium range total count: 164 / NOE sequential total count: 225 / Hydrogen bond constraints total count: 96 / Protein chi angle constraints total count: 0 / Protein phi angle constraints total count: 108 / Protein psi angle constraints total count: 108 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.732 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5.25 ° / Maximum upper distance constraint violation: 0.33 Å | ||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0187 Å / Distance rms dev error: 0.002 Å |