+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5342 | |||||||||
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Title | DNA-free p53 Tetramer Reconstruction | |||||||||
Map data | DNA-free p53 Tetramer Reconstruction | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining | |||||||||
Authors | Pham N / Lucumi A / Cheung N / Viadiu H | |||||||||
Citation | Journal: Biochemistry / Year: 2012 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5342.map.gz | 5.6 MB | EMDB map data format | |
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Header (meta data) | emd-5342-v30.xml emd-5342.xml | 7.4 KB 7.4 KB | Display Display | EMDB header |
Images | emd_5342_1.jpg | 69.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5342 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5342 | HTTPS FTP |
-Validation report
Summary document | emd_5342_validation.pdf.gz | 76.8 KB | Display | EMDB validaton report |
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Full document | emd_5342_full_validation.pdf.gz | 75.9 KB | Display | |
Data in XML | emd_5342_validation.xml.gz | 498 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5342 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5342 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5342.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | DNA-free p53 Tetramer Reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET28 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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 |
-Image processing
Final reconstruction | Number images used: 8550 |
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Final two d classification | Number classes: 50 |