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Yorodumi- PDB-1ycq: XENOPUS LAEVIS MDM2 BOUND TO THE TRANSACTIVATION DOMAIN OF HUMAN P53 -
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-Basic information
Entry | Database: PDB / ID: 1ycq | ||||||
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Title | XENOPUS LAEVIS MDM2 BOUND TO THE TRANSACTIVATION DOMAIN OF HUMAN P53 | ||||||
Components |
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Keywords | COMPLEX (ONCOGENE PROTEIN/PEPTIDE) / ANTI-ONCOGENE / DNA-BINDING / TRANSCRIPTION REGULATION / NUCLEAR PROTEIN / COMPLEX (ONCOGENE PROTEIN-PEPTIDE) / PHOSPHORYLATION / ACTIVATOR / COMPLEX (ONCOGENE PROTEIN-PEPTIDE) complex | ||||||
Function / homology | Function and homology information regulation of biological quality / 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 / regulation of fibroblast apoptotic process / 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 ...regulation of biological quality / 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 / regulation of fibroblast apoptotic process / 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 / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / circadian behavior / mRNA transcription / bone marrow development / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / germ cell nucleus / T cell lineage commitment / 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 / 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 / B cell lineage commitment / thymocyte apoptotic process / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / positive regulation of cardiac muscle cell apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / ER overload response / negative regulation of DNA replication / positive regulation of release of cytochrome c from mitochondria / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / positive regulation of execution phase of apoptosis / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to X-ray / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / Pyroptosis / replicative senescence / mitophagy / cellular response to UV-C / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / hematopoietic stem cell differentiation / somitogenesis / embryonic organ development / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chromosome organization / T cell proliferation involved in immune response / hematopoietic progenitor cell differentiation / glial cell proliferation / type II interferon-mediated signaling pathway / cis-regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to glucose starvation / viral process / cellular response to actinomycin D / positive regulation of intrinsic apoptotic signaling pathway / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / mitotic G1 DNA damage checkpoint signaling / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / tumor necrosis factor-mediated signaling pathway / response to salt stress / cardiac muscle cell apoptotic process / Regulation of TP53 Activity through Acetylation Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Kussie, P.H. / Pavletich, N.P. | ||||||
Citation | Journal: Science / Year: 1996 Title: Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Authors: Kussie, P.H. / Gorina, S. / Marechal, V. / Elenbaas, B. / Moreau, J. / Levine, A.J. / Pavletich, N.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ycq.cif.gz | 32.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ycq.ent.gz | 21.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ycq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ycq_validation.pdf.gz | 376.4 KB | Display | wwPDB validaton report |
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Full document | 1ycq_full_validation.pdf.gz | 378.3 KB | Display | |
Data in XML | 1ycq_validation.xml.gz | 3.5 KB | Display | |
Data in CIF | 1ycq_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/1ycq ftp://data.pdbj.org/pub/pdb/validation_reports/yc/1ycq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12165.851 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P56273 |
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#2: Protein/peptide | Mass: 2018.246 Da / Num. of mol.: 1 / Fragment: RESIDUES 13 - 29 Source method: isolated from a genetically manipulated source References: UniProt: P04637 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.56 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 6257 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.055 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. measured all: 15953 |
-Processing
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Refinement | Resolution: 2.3→7 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.3→7 Å
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