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- EMDB-5342: DNA-free p53 Tetramer Reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-5342
TitleDNA-free p53 Tetramer Reconstruction
Map dataDNA-free p53 Tetramer Reconstruction
Sample
  • Sample: p53
  • Protein or peptide: p53
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining
AuthorsPham N / Lucumi A / Cheung N / Viadiu H
CitationJournal: 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
DepositionSep 25, 2011-
Header (metadata) releaseNov 28, 2011-
Map releaseFeb 13, 2013-
UpdateFeb 13, 2013-
Current statusFeb 13, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.157
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.157
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5342_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5342.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDNA-free p53 Tetramer Reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 120 pix.
= 264. Å		2.2 Å/pix.
x 120 pix.
= 264. Å		2.2 Å/pix.
x 120 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.157 / Movie #1: 0.157
Minimum - Maximum-0.03884156 - 0.70010084
Average (Standard dev.)0.00812203 (±0.05045742)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-60
Dimensions120120120
Spacing120120120
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
D min/max/mean-0.0390.7000.008

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Supplemental data

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Sample components

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Entire : p53

EntireName: p53
Components
  • Sample: p53
  • Protein or peptide: p53

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Supramolecule #1000: p53

SupramoleculeName: p53 / type: sample / ID: 1000 / Oligomeric state: tetramer / Number unique components: 1
Molecular weightExperimental: 200 KDa / Theoretical: 200 KDa / Method: Gel filtration

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Macromolecule #1: p53

MacromoleculeName: p53 / type: protein_or_peptide / ID: 1 / Name.synonym: p53 / Number of copies: 4 / Oligomeric state: Tetramer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Nucleus
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET28

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7 / Details: 150mM NaCl
StainingType: NEGATIVE / Details: 1% uranyl formate
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI SPHERA
Image recordingNumber real images: 50
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: PHILIPS ROTATION HOLDER

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Image processing

Final reconstructionNumber images used: 8550
Final two d classificationNumber classes: 50

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