+Open data
-Basic information
Entry | Database: PDB / ID: 2bio | ||||||
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Title | human p53 core domain mutant M133L-V203A-N239Y-R249S-N268D | ||||||
Components | CELLULAR TUMOR ANTIGEN P53 | ||||||
Keywords | DNA BINDING PROTEIN / ACTIVATOR / ANTI-ONCOGENE / APOPTOSIS / DISEASE MUTATION / DNA-BINDING / DNA-BINDING PROTEIN / LI-FRAUMENI SYNDROME / NUCLEAR PROTEIN / P53 DNA-BINDING DOMAIN / PHOSPHORYLATION / POLYMORPHISM / SECOND-SITE SUPPRESSOR MUTATION / SUPERSTABLE MUTANT / TRANSCRIPTION REGULATION / TUMOR SUPPRESSOR | ||||||
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 / 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 / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / 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 / 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 / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / 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 / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to actinomycin D / somitogenesis / type II interferon-mediated signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription initiation-coupled chromatin remodeling / 14-3-3 protein binding / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation / response to salt stress Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Joerger, A.C. / Fersht, A.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structures of P53 Cancer Mutants and Mechanism of Rescue by Second-Site Suppressor Mutations Authors: Joerger, A.C. / Ang, H.C. / Veprintsev, D.B. / Blair, C.M. / Fersht, A.R. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Crystal Structure of a Superstable Mutant of Human P53 Core Domain: Insights Into the Mechanism of Rescuing Oncogenic Mutations Authors: Joerger, A.C. / Allen, M.D. / Fersht, A.R. #2: Journal: Science / Year: 1994 Title: Crystal Structure of a P53 Tumor Suppressor-DNA Complex: Understanding Tumorigenic Mutations Authors: Cho, Y. / Gorina, S. / Jeffrey, P.D. / 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 | 2bio.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bio.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 2bio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bio_validation.pdf.gz | 427.6 KB | Display | wwPDB validaton report |
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Full document | 2bio_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | 2bio_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 2bio_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/2bio ftp://data.pdbj.org/pub/pdb/validation_reports/bi/2bio | HTTPS FTP |
-Related structure data
Related structure data | 2bimC 2binC 2bipC 2biqC 1uolS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 24520.727 Da / Num. of mol.: 1 / Fragment: DNA-BINDING (CORE) DOMAIN, RESIDUES 94-312 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04637 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.11 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→26.6 Å / Num. obs: 16731 / % possible obs: 99.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.5 / % possible all: 98.9 |
-Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UOL Resolution: 1.9→26.6 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 1.9→26.6 Å
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Refine LS restraints |
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