+Open data
-Basic information
Entry | Database: PDB / ID: 8f2h | ||||||||||||
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Title | Wild type P53 dimer structure from human cancer cells | ||||||||||||
Components | Cellular tumor antigen p53 | ||||||||||||
Keywords | ANTITUMOR PROTEIN / cancer / tumor suppressor / cell cycle / apoptosis / DNA repair | ||||||||||||
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 / 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 ...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 / 14-3-3 protein binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||
Authors | Solares, M. / Kelly, D.F. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Chembiochem / Year: 2022 Title: High-Resolution Imaging of Human Cancer Proteins Using Microprocessor Materials. Authors: Maria J Solares / G M Jonaid / William Y Luqiu / Samantha Berry / Janki Khadela / Yanping Liang / Madison C Evans / Kevin J Pridham / William J Dearnaley / Zhi Sheng / Deborah F Kelly / Abstract: Mutations in tumor suppressor genes, such as Tumor Protein 53 (TP53), are heavily implicated in aggressive cancers giving rise to gain- and loss-of-function phenotypes. While individual domains of ...Mutations in tumor suppressor genes, such as Tumor Protein 53 (TP53), are heavily implicated in aggressive cancers giving rise to gain- and loss-of-function phenotypes. While individual domains of the p53 protein have been studied extensively, structural information for full-length p53 remains incomplete. Functionalized microprocessor chips (microchips) with properties amenable to electron microscopy permitted us to visualize complete p53 assemblies for the first time. The new structures revealed p53 in an inactive dimeric state independent of DNA binding. Residues located at the protein-protein interface corresponded with modification sites in cancer-related hot spots. Changes in these regions may amplify the toxic effects of clinical mutations. Taken together, these results contribute advances in technology and imaging approaches to decode native protein models in different states of activation. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f2h.cif.gz | 251.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f2h.ent.gz | 201.9 KB | Display | PDB format |
PDBx/mmJSON format | 8f2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f2h_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8f2h_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8f2h_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 8f2h_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/8f2h ftp://data.pdbj.org/pub/pdb/validation_reports/f2/8f2h | HTTPS FTP |
-Related structure data
Related structure data | 28816MC 8f2iC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 43711.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: U87-MG / Organ: brain tumor / Plasmid details: glioblastoma / Variant: wild type / Tissue: brain / References: UniProt: P04637 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: P53 dimer isolated from U87-MG cells / Type: CELL / Details: Native protein, wild-type with no tags / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) / Cellular location: nucleus / Organ: Brain / Organelle: nucleus / Tissue: Brain tumor |
Buffer solution | pH: 7.5 Details: 20 mM HEPES (pH 7.5), 140 mM NaCl, 2 mM MgCl2, 2 mM CaCl2, 5 mM imidazole |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Sample was placed on Silicon nitride chips coated with Ni-NTA layers |
Specimen support | Details: Silicon nitride chips coated with Ni-NTA layers prior to sample application Grid material: SILICON NITRIDE / Grid type: Homemade |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K Details: The microchip samples were loaded into a FEI Mark III Vitrobot and flash-frozen into liquid ethane. |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: TFS TALOS F200C |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 142000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 5 e/Å2 / Film or detector model: FEI CETA (4k x 4k) / Num. of grids imaged: 10 / Num. of real images: 300 |
Image scans | Sampling size: 14 µm |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 8000 | |||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8000 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | B value: 50 / Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||
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