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 / regulation of mitochondrial membrane permeability / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / negative regulation of protein localization to plasma membrane / positive regulation of mitochondrial membrane permeability / regulation of growth / 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 / NFE2L2 regulating tumorigenic genes / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / response to cycloheximide / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / B cell lineage commitment / 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 / negative regulation of reproductive process / cardiac septum morphogenesis / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / BH3 domain binding / germ cell development / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / apoptotic mitochondrial changes / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / negative regulation of anoikis / 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 / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C Similarity search - Function
Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
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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
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-15N HSQC
1
2
2
2D 1H-15N HSQC
1
3
3
2D 1H-15N HSQC
1
4
4
2D 1H-15N HSQC
1
5
5
2D 1H-15N HSQC
1
6
5
2D 1H-15N HSQC
1
7
7
2D 1H-15N HSQC
1
8
8
2D 1H-15N HSQC
1
9
9
2D 1H-15N HSQC
1
10
10
2D 1H-15N HSQC
1
11
2
3D 1H-15N NOESY
1
12
1
3D HNCA
1
13
1
3D HN(CA)CB
1
14
1
3D HNCO
1
15
1
3DHN(CO)CA
1
16
1
2D 1H-13C HSQC aliphatic
1
17
1
3D (H)CCH-TOCSY
1
18
1
3D 1H-13C NOESY aliphatic
1
19
2
2D 1H-13C HSQC aliphatic
1
20
9
2DCBCACO
1
21
10
2DCBCACO
1
22
9
2D 1H-13C HSQC aliphatic
1
23
10
2D 1H-13C HSQC aliphatic
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.
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... andKollman
refinement
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
+
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