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Yorodumi- PDB-6rz3: Crystal structure of a complex between the DNA-binding domain of ... -
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-Basic information
Entry | Database: PDB / ID: 6rz3 | ||||||
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Title | Crystal structure of a complex between the DNA-binding domain of p53 and the carboxyl-terminal conserved region of iASPP | ||||||
Components |
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Keywords | ANTITUMOR PROTEIN / Complex / p53 / iASPP | ||||||
Function / homology | Function and homology information multicellular organismal-level homeostasis / cardiac right ventricle morphogenesis / embryonic camera-type eye development / hair cycle / ventricular cardiac muscle tissue development / 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 ...multicellular organismal-level homeostasis / cardiac right ventricle morphogenesis / embryonic camera-type eye development / hair cycle / ventricular cardiac muscle tissue development / 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 / 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 / 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 / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / intercellular bridge / negative regulation of DNA replication / ER overload response / B cell lineage commitment / 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 / cardiac septum morphogenesis / 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 / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / mitophagy / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / : / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / chromosome organization / positive regulation of RNA polymerase II transcription preinitiation complex assembly / T cell proliferation involved in immune response / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / glial cell proliferation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / embryonic organ development / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to actinomycin D / somitogenesis / type II interferon-mediated signaling pathway / cellular response to glucose starvation / cardiac muscle contraction / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.23 Å | ||||||
Authors | Chen, S. / Ren, J. / Jones, E.Y. / Lu, X. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: iASPP mediates p53 selectivity through a modular mechanism fine-tuning DNA recognition. Authors: Chen, S. / Wu, J. / Zhong, S. / Li, Y. / Zhang, P. / Ma, J. / Ren, J. / Tan, Y. / Wang, Y. / Au, K.F. / Siebold, C. / Bond, G.L. / Chen, Z. / Lu, M. / Jones, E.Y. / Lu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rz3.cif.gz | 162.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rz3.ent.gz | 128.7 KB | Display | PDB format |
PDBx/mmJSON format | 6rz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rz3_validation.pdf.gz | 437.6 KB | Display | wwPDB validaton report |
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Full document | 6rz3_full_validation.pdf.gz | 438.9 KB | Display | |
Data in XML | 6rz3_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 6rz3_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/6rz3 ftp://data.pdbj.org/pub/pdb/validation_reports/rz/6rz3 | 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: 25660.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04637 |
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#2: Protein | Mass: 26131.959 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R13L, IASPP, NKIP1, PPP1R13BL, RAI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WUF5 |
#3: Chemical | ChemComp-ZN / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.55 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 18% (w/v) polyethylene glycol 3350, 0.18 M tri-sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 4.23→30 Å / Num. obs: 4819 / % possible obs: 93.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 4.23→4.4 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 329 / % possible all: 94.7 |
Serial crystallography sample delivery | Method: fixed target |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VGE, 2XWR Resolution: 4.23→29.8 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.888 / SU B: 160.302 / SU ML: 0.848 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.063 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 378.53 Å2 / Biso mean: 195.602 Å2 / Biso min: 127.27 Å2
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Refinement step | Cycle: final / Resolution: 4.23→29.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.232→4.341 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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