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- EMDB-1896: EM map of the specific p53-DNA complex at 21 angstroms resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-1896
TitleEM map of the specific p53-DNA complex at 21 angstroms resolution
Map data3D EM map of the specific p53-DNA complex
Sample
  • Sample: Murine p53 tetramer complexed with specific DNA construct
  • Protein or peptide: p53
  • DNA: DNA
Keywordscryo electron microscopy / p53 / single particle analysis / transcription factor
Biological speciesMus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsAramayo R / Sherman MB / Brownless K / Lurz R / Okorokov AL / Orlova EV
CitationJournal: Nucleic Acids Res / Year: 2011
Title: Quaternary structure of the specific p53-DNA complex reveals the mechanism of p53 mutant dominance.
Authors: Ricardo Aramayo / Michael B Sherman / Kathryne Brownless / Rudi Lurz / Andrei L Okorokov / Elena V Orlova /
Abstract: The p53 tumour suppressor is a transcriptional activator that controls cell fate in response to various stresses. p53 can initiate cell cycle arrest, senescence and/or apoptosis via transactivation ...The p53 tumour suppressor is a transcriptional activator that controls cell fate in response to various stresses. p53 can initiate cell cycle arrest, senescence and/or apoptosis via transactivation of p53 target genes, thus preventing cancer onset. Mutations that impair p53 usually occur in the core domain and negate the p53 sequence-specific DNA binding. Moreover, these mutations exhibit a dominant negative effect on the remaining wild-type p53. Here, we report the cryo electron microscopy structure of the full-length p53 tetramer bound to a DNA-encoding transcription factor response element (RE) at a resolution of 21 A. While two core domains from both dimers of the p53 tetramer interact with DNA within the complex, the other two core domains remain available for binding another DNA site. This finding helps to explain the dominant negative effect of p53 mutants based on the fact that p53 dimers are formed co-translationally before the whole tetramer assembles; therefore, a single mutant dimer would prevent the p53 tetramer from binding DNA. The structure indicates that the Achilles' heel of p53 is in its dimer-of-dimers organization, thus the tetramer activity can be negated by mutation in only one allele followed by tumourigenesis.
History
DepositionMay 14, 2011-
Header (metadata) releaseAug 24, 2011-
Map releaseAug 24, 2011-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

em-1896.png

Downloads & links

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Map

FileDownload / File: emd_1896.map.gz / Format: CCP4 / Size: 2.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D EM map of the specific p53-DNA complex
Voxel sizeX=Y=Z: 2.48 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-3.5755 - 13.3706
Average (Standard dev.)0.0000000303295 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-44-45-45
Dimensions909090
Spacing909090
CellA=B=C: 223.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.482.482.48
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z223.200223.200223.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-45-44-45
NC/NR/NS909090
D min/max/mean-3.57513.3710.000

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Supplemental data

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Sample components

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Entire : Murine p53 tetramer complexed with specific DNA construct

EntireName: Murine p53 tetramer complexed with specific DNA construct
Components
  • Sample: Murine p53 tetramer complexed with specific DNA construct
  • Protein or peptide: p53
  • DNA: DNA

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Supramolecule #1000: Murine p53 tetramer complexed with specific DNA construct

SupramoleculeName: Murine p53 tetramer complexed with specific DNA construct
type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 240 KDa / Theoretical: 240 KDa

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Macromolecule #1: p53

MacromoleculeName: p53 / type: protein_or_peptide / ID: 1 / Name.synonym: p53
Details: Murine p53 tetramer bound to a specific DNA construct
Number of copies: 4 / Oligomeric state: Tetramer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House Mouse
Molecular weightExperimental: 240 KDa / Theoretical: 240 KDa
Recombinant expressionOrganism: unidentified baculovirus

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Macromolecule #2: DNA

MacromoleculeName: DNA / type: dna / ID: 2 / Name.synonym: DNA / Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: synthetic construct (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7 / Details: 100mM NaCl, 25mM Tris-HCl, 1mM DTT
VitrificationCryogen name: ETHANE / Chamber temperature: 80 K / Instrument: OTHER / Method: Blot few seconds before plunging

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 5.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 90 K
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 10 e/Å2

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Image processing

CTF correctionDetails: Phase flipping
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, EMAN

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