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Yorodumi- PDB-2ly4: HMGB1-facilitated p53 DNA binding occurs via HMG-box/p53 transact... -
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-Basic information
Entry | Database: PDB / ID: 2ly4 | ||||||
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Title | HMGB1-facilitated p53 DNA binding occurs via HMG-box/p53 transactivation domain interaction and is regulated by the acidic tail | ||||||
Components |
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Keywords | NUCLEAR PROTEIN/ANTITUMOUR PROTEIN / HMG / p53 / TAD / NUCLEAR PROTEIN-ANTITUMOUR PROTEIN complex | ||||||
Function / homology | Function and homology information regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / myeloid dendritic cell activation / T-helper 1 cell activation / T-helper 1 cell differentiation ...regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / myeloid dendritic cell activation / T-helper 1 cell activation / T-helper 1 cell differentiation / C-X-C chemokine binding / positive regulation of dendritic cell differentiation / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of toll-like receptor 9 signaling pathway / neutrophil clearance / positive regulation of DNA ligation / positive regulation of interleukin-1 production / RAGE receptor binding / Regulation of TLR by endogenous ligand / bubble DNA binding / alphav-beta3 integrin-HMGB1 complex / V(D)J recombination / Apoptosis induced DNA fragmentation / positive regulation of chemokine (C-X-C motif) ligand 2 production / inflammatory response to antigenic stimulus / supercoiled DNA binding / MyD88 deficiency (TLR2/4) / 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 / positive regulation of monocyte chemotaxis / 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 / apoptotic cell clearance / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / dendritic cell chemotaxis / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / DNA binding, bending / 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 / IRAK4 deficiency (TLR2/4) / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / positive regulation of vascular endothelial cell proliferation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / phosphatidylserine binding / negative regulation of DNA replication / ER overload response / positive regulation of activated T cell proliferation / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell 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 / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / chemoattractant activity / PI5P Regulates TP53 Acetylation / negative regulation of blood vessel endothelial cell migration / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / TRAF6 mediated NF-kB activation / rRNA transcription / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Authors | Rowell, J.P. / Simpson, K.L. / Stott, K. / Watson, M. / Thomas, J.O. | ||||||
Citation | Journal: Structure / Year: 2012 Title: HMGB1-Facilitated p53 DNA Binding Occurs via HMG-Box/p53 Transactivation Domain Interaction, Regulated by the Acidic Tail. Authors: Rowell, J.P. / Simpson, K.L. / Stott, K. / Watson, M. / Thomas, J.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ly4.cif.gz | 408.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ly4.ent.gz | 352.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ly4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/2ly4 ftp://data.pdbj.org/pub/pdb/validation_reports/ly/2ly4 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9705.185 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HMG1, HMGB1 / Plasmid: pT7-7 HMG1-A / Production host: Escherichia coli (E. coli) / References: UniProt: P09429 |
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#2: Protein | Mass: 9981.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: P53, TP53 / Plasmid: pET16b-p53(1-93) / Production host: Escherichia coli (E. coli) / References: UniProt: P04637 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 10 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 0.5 mM PMSF, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.01 / 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: DGSA-distance geometry simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |