+Open data
-Basic information
Entry | Database: PDB / ID: 1ycs | ||||||
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Title | P53-53BP2 COMPLEX | ||||||
Components |
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Keywords | COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) / ANKYRIN REPEATS / SH3 / P53 / TUMOR SUPPRESSOR / MULTIGENE FAMILY / NUCLEAR PROTEIN / PHOSPHORYLATION / DISEASE MUTATION / POLYMORPHISM / COMPLEX (ANTI-ONCOGENE-ANKYRIN REPEATS) / COMPLEX (ANTI-ONCOGENE-ANKYRIN REPEATS) complex | ||||||
Function / homology | Function and homology information 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 ...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 / 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 / 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 / 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 / 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 / negative regulation of DNA replication / ER overload response / 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 / PI5P Regulates TP53 Acetylation / 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 / rRNA transcription / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / negative regulation of cell cycle / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / NF-kappaB binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / chromosome organization / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / MDM2/MDM4 family protein binding / glial cell proliferation / embryonic organ development / cellular response to glucose starvation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / cardiac muscle cell apoptotic process / response to salt stress / transcription initiation-coupled chromatin remodeling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Gorina, S. / Pavletich, N.P. | ||||||
Citation | Journal: Science / Year: 1996 Title: Structure of the p53 tumor suppressor bound to the ankyrin and SH3 domains of 53BP2. Authors: Gorina, S. / Pavletich, N.P. #1: Journal: Mol.Cell.Biol. / Year: 1996 Title: The P53-Binding Protein 53BP2 Also Interacts with Bcl2 and Impedes Cell Cycle Progression at G2/M Authors: Naumovski, L. / Cleary, M.L. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Two Cellular Proteins that Bind to Wild-Type But not Mutant P53 Authors: Iwabuchi, K. / Bartel, P.L. / Li, B. / Marraccino, R. / Fields, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ycs.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ycs.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ycs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/1ycs ftp://data.pdbj.org/pub/pdb/validation_reports/yc/1ycs | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22448.531 Da / Num. of mol.: 1 / Fragment: RESIDUES 97 - 287 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: RESIDUES 291-529 / Plasmid: PET3D / Gene (production host): RESIDUES 94-292 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (D3) / References: UniProt: P04637 |
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#2: Protein | Mass: 26943.475 Da / Num. of mol.: 1 / Fragment: RESIDUES 327 - 519 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: THE FRAGMENT USED IN THE CRYSTALLIZATION (RESIDUES 291-519) WAS PRODUCED BY THE CLEAVAGE OF FACTOR XA FROM GST-FUSION PROTEIN Cell line: BL21 / Gene: RESIDUES 291-529 / Plasmid: PGEX-3X, GST FUSION / Gene (production host): RESIDUES 291-529 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (D3) / References: UniProt: Q13625 |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.21 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92 |
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Detector | Detector: CCD / Date: Dec 22, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Num. obs: 30230 / % possible obs: 99.1 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.057 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. measured all: 220654 |
-Processing
Software |
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Refinement | Resolution: 2.2→7 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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