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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22827 | ||||||||||||
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Title | P53 tetramer from Glioblastoma | ||||||||||||
![]() | P53 tetramer from Glioblastoma | ||||||||||||
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Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.0 Å | ||||||||||||
![]() | Solares MJ / Kelly DF | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Microchip-Based Structure Determination of Disease-Relevant p53. Authors: Maria J Solares / G M Jonaid / William Y Luqiu / Yanping Liang / Madison C Evans / William J Dearnaley / Zhi Sheng / Deborah F Kelly / ![]() Abstract: The tumor suppressor protein TP53 (p53) plays a multifaceted role in all cells of the human body. Mutations in the gene are often involved in cancer induction and disease progression. Despite its ...The tumor suppressor protein TP53 (p53) plays a multifaceted role in all cells of the human body. Mutations in the gene are often involved in cancer induction and disease progression. Despite its important role in health and development, structural information for p53 remains incomplete. Here, we present a microchip-based technology to facilitate structural studies of p53 assemblies derived from human cancer cells. These devices do not introduce foreign sequences to the gene and maintain naturally occurring post-translational modifications. Using cryo-electron microscopy, structures for the p53 monomer (∼50 kDa) and tetramer (∼200 kDa) were resolved to ∼4.8 and ∼7 Å, respectively. These structures revealed new insights for flexible regions of p53 along with biologically relevant ubiquitination sites. Collectively, the convergence of nanotechnology tools and structural imaging builds a strong framework to understand the oncogenic impact of p53 in human tissues. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 10.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.5 KB 13.5 KB | Display Display | ![]() |
Images | ![]() | 178.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.1 KB | Display | ![]() |
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Full document | ![]() | 77.2 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | P53 tetramer from Glioblastoma | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Tetramer of p53 and DNA
Entire | Name: Tetramer of p53 and DNA |
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Components |
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-Supramolecule #1: Tetramer of p53 and DNA
Supramolecule | Name: Tetramer of p53 and DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: isolated from glioblastoma cells |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: Tumor suppressor protein, P53
Macromolecule | Name: Tumor suppressor protein, P53 / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: ![]() |
Sequence | String: MEEPQSDPSV EPPLSQETFS DLWKLLPENN VLSPLPSQAM DDLMLSPDDI EQWFTEDPGP DEAPRMPEA APPVAPAPAA PTPAAPAPAP SWPLSSSVPS QKTYQGSYGF RLGFLHSGTA K SVTCTYSP ALNKMFCQLA KTCPVQLWVD STPPPGTRVR AMAIYKQSQH ...String: MEEPQSDPSV EPPLSQETFS DLWKLLPENN VLSPLPSQAM DDLMLSPDDI EQWFTEDPGP DEAPRMPEA APPVAPAPAA PTPAAPAPAP SWPLSSSVPS QKTYQGSYGF RLGFLHSGTA K SVTCTYSP ALNKMFCQLA KTCPVQLWVD STPPPGTRVR AMAIYKQSQH MTEVVRRCPH HE RCSDSDG LAPPQHLIRV EGNLRVEYLD DRNTFRHSVV VPYEPPEVGS DCTTIHYNYM CNS SCMGGM NRRPILTIIT LEDSSGNLLG RNSFEVRVCA CPGRDRRTEE ENLRKKGEPH HELP PGSTK RALPNNTSSS PQPKKKPLDG EYFTLQIRGR ERFEMFRELN EALELKDAQA GKEPG GSRA HSSHLKSKKG QSTSRHKKLM FKTEGPDSD |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.2 Details: 20 mM HEPES, (pH 7.2), 140 mM NaCl, 2 mM CaCl2, 2 mM MgCl2, and 5 mM imidazole |
Grid | Material: SILICON NITRIDE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III / Details: blotted for 6 seconds before plunging. |
Details | Concentrated onto 25% Ni-NTA coating on silicon nitride microchips |
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Electron microscopy
Microscope | TFS TALOS F200C |
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Image recording | Film or detector model: FEI CETA (4k x 4k) / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 2 / Number real images: 150 / Average exposure time: 1.0 sec. / Average electron dose: 5.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 92000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 92000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |