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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5342 | |||||||||
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Title | DNA-free p53 Tetramer Reconstruction | |||||||||
![]() | DNA-free p53 Tetramer Reconstruction | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / negative staining | |||||||||
![]() | Pham N / Lucumi A / Cheung N / Viadiu H | |||||||||
![]() | ![]() Title: The tetramer of p53 in the absence of DNA forms a relaxed quaternary state. Authors: Nam Pham / Armando Lucumi / Nikki Cheung / Hector Viadiu / ![]() Abstract: p53 is a tetrameric multidomain protein that triggers the anticancer cellular response to stress. We have calculated a three-dimensional reconstruction of full-length human p53 in the absence of DNA ...p53 is a tetrameric multidomain protein that triggers the anticancer cellular response to stress. We have calculated a three-dimensional reconstruction of full-length human p53 in the absence of DNA using single-particle electron microscopy. The reconstruction of DNA-free full-length p53 shows a square-shaped structure with four distinct domains and a hollow center. In comparison with the known compacted DNA-bound full-length p53 structures, the DNA-free p53 tetramer adopts a relaxed conformation with separated monomers and oligomerization interfaces different from those of the DNA-bound conformation. | |||||||||
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 | ![]() | 5.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 7.4 KB 7.4 KB | Display Display | ![]() |
Images | ![]() | 69.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 76.8 KB | Display | ![]() |
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Full document | ![]() | 75.9 KB | Display | |
Data in XML | ![]() | 498 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | DNA-free p53 Tetramer Reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 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 : p53
Entire | Name: p53 |
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Components |
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-Supramolecule #1000: p53
Supramolecule | Name: p53 / type: sample / ID: 1000 / Oligomeric state: tetramer / Number unique components: 1 |
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Molecular weight | Experimental: 200 KDa / Theoretical: 200 KDa / Method: Gel filtration |
-Macromolecule #1: p53
Macromolecule | Name: p53 / type: protein_or_peptide / ID: 1 / Name.synonym: p53 / Number of copies: 4 / Oligomeric state: Tetramer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7 / Details: 150mM NaCl |
Staining | Type: NEGATIVE / Details: 1% uranyl formate |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | FEI TECNAI SPHERA |
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Image recording | Number real images: 50 |
Electron beam | Acceleration voltage: 200 kV / Electron source: LAB6 |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Eucentric / Specimen holder model: PHILIPS ROTATION HOLDER |
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Image processing
Final reconstruction | Number images used: 8550 |
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Final two d classification | Number classes: 50 |