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Yorodumi- PDB-2mej: Solution Structure of the Complex Between BCL-xL and the p53 Core... -
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-Basic information
Entry | Database: PDB / ID: 2mej | ||||||
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Title | Solution Structure of the Complex Between BCL-xL and the p53 Core Domain determined with PRE restraints | ||||||
Components |
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Keywords | APOPTOSIS / BCL-xL / p53 / BCL-2 family / cytoplasmic p53 / selective labeling | ||||||
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 / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / regulation of mitochondrial membrane permeability / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / regulation of growth / negative regulation of protein localization to plasma membrane / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Bcl-2 family protein complex / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / BH domain binding / NFE2L2 regulating tumorigenic genes / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / response to cycloheximide / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / ER overload response / negative regulation of DNA replication / STAT5 activation downstream of FLT3 ITD mutants / B cell lineage commitment / cellular response to alkaloid / hepatocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / thymocyte apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / mitotic G1 DNA damage checkpoint signaling / cardiac septum morphogenesis / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / BH3 domain binding / germ cell development / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / negative regulation of anoikis / mitophagy / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / replicative senescence Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Authors | Viacava Follis, A. / Grace, C.R. / Kriwacki, R.W. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mej.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2mej.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 2mej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mej_validation.pdf.gz | 536.6 KB | Display | wwPDB validaton report |
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Full document | 2mej_full_validation.pdf.gz | 854.3 KB | Display | |
Data in XML | 2mej_validation.xml.gz | 138.1 KB | Display | |
Data in CIF | 2mej_validation.cif.gz | 180.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/2mej ftp://data.pdbj.org/pub/pdb/validation_reports/me/2mej | 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: 23669.945 Da / Num. of mol.: 1 / Fragment: UNP residues 1-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07817 |
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#2: Protein | Mass: 24412.721 Da / Num. of mol.: 1 / Fragment: UNP residues 96-312 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04637 |
#3: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: SOLUTION STRUCTURE OF THE KINETICALLY LABILE COMPLEX BETWEEN THE DNA BINDING DOMAIN OF P53 AND BCL-XL DETERMINED USING PARAMAGNETIC RELAXATION ENHANCEMENT AND LIMITED NOE CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: HADDOCK STARTING STRUCTURES: FOR CHAIN A (BCL-XL), THE LOWEST ENERGY CONFORMER OF PDB ENTRY 2ME8 DEPOSITED BY THE AUTHORS; FOR CHAIN B (P53 DNA BINDING DOMAIN), CHAIN C OF PDB ENTRY 2AC0, THE P53 CRYSTAL STRUCTURE. |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.05 / pH: 7 / 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: 13 / NOE intraresidue total count: 0 / NOE long range total count: 13 / NOE medium range total count: 0 / NOE sequential total count: 0 / Hydrogen bond constraints total count: 0 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 0 / Protein psi angle constraints total count: 0 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 1.39 Å | ||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.13 Å / Distance rms dev error: 0.06 Å |