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- EMDB-8927: Wild-type p53-DNA assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-8927
TitleWild-type p53-DNA assembly
Map dataWild-type p53-DNA assembly
Sample
  • Complex: Wild-type p53-DNA assembly
    • Protein or peptide: Wild-type p53-DNA assembly
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.1 Å
AuthorsKelly DF / Dearnaley WJ / Liang Y
CitationJournal: DNA Repair (Amst) / Year: 2019
Title: Correcting errors in the BRCA1 warning system.
Authors: Yanping Liang / William J Dearnaley / Nick A Alden / Maria J Solares / Brian L Gilmore / Kevin J Pridham / A Cameron Varano / Zhi Sheng / Elizabeth Alli / Deborah F Kelly /
Abstract: Given its important role in human health and disease, remarkably little is known about the full-length three-dimensional (3D) molecular architecture of the breast cancer type 1 susceptibility protein ...Given its important role in human health and disease, remarkably little is known about the full-length three-dimensional (3D) molecular architecture of the breast cancer type 1 susceptibility protein (BRCA1), or its mechanisms to engage the tumor suppressor, TP53 (p53). Here, we show how a prevalent cancer-related mutation in the C-terminal region of the full-length protein, BRCA1, affects its structural properties, yet can be biochemically corrected to restore its functional capacity. As a downstream consequence of restoring the ubiquitin ligase activity of mutated BRCA1, the DNA repair response of p53 was enhanced in cellular extracts naturally deficient in BRCA1 protein expression. Complementary structural insights of p53 tetramers bound to DNA in different stage of the repair process support these biochemical findings in the context of human cancer cells. Equally important, we show how this knowledge can be used to lower the viability of breast cancer cells by modulating the stability of the BRCA1 protein and its associated players.
History
DepositionJun 29, 2018-
Header (metadata) releaseJul 11, 2018-
Map releaseDec 19, 2018-
UpdateJan 9, 2019-
Current statusJan 9, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.552
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.552
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8927.png

Downloads & links

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Map

FileDownload / File: emd_8927.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWild-type p53-DNA assembly
Voxel sizeX=Y=Z: 3.2 Å
Density
Contour LevelBy AUTHOR: 0.552 / Movie #1: 0.552
Minimum - Maximum-1.0355337 - 2.7917774
Average (Standard dev.)0.016378205 (±0.10583128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 320.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.23.23.2
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z320.000320.000320.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-1.0362.7920.016

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Supplemental data

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Sample components

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Entire : Wild-type p53-DNA assembly

EntireName: Wild-type p53-DNA assembly
Components
  • Complex: Wild-type p53-DNA assembly
    • Protein or peptide: Wild-type p53-DNA assembly

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Supramolecule #1: Wild-type p53-DNA assembly

SupramoleculeName: Wild-type p53-DNA assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Organ: Brain / Tissue: Brain
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Wild-type p53-DNA assembly

MacromoleculeName: Wild-type p53-DNA assembly / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Human (human) / Organ: Brain / Tissue: Brain
SequenceString: MEEPQSDPSV EPPLSQETFS DLWKLLPENN VLSPLPSQAM DDLMLSPDDI EQWFTEDPGP DEAPRMPEAA PPVAPAPAAP TPAAPAPAPS WPLSSSVPSQ KTYQGSYGFR LGFLHSGTAK SVTCTYSPAL NKMFCQLAKT CPVQLWVDST PPPGTRVRAM AIYKQSQHMT ...String:
MEEPQSDPSV EPPLSQETFS DLWKLLPENN VLSPLPSQAM DDLMLSPDDI EQWFTEDPGP DEAPRMPEAA PPVAPAPAAP TPAAPAPAPS WPLSSSVPSQ KTYQGSYGFR LGFLHSGTAK SVTCTYSPAL NKMFCQLAKT CPVQLWVDST PPPGTRVRAM AIYKQSQHMT EVVRRCPHHE RCSDSDGLAP PQHLIRVEGN LRVEYLDDRN TFRHSVVVPY EPPEVGSDCT TIHYNYMCNS SCMGGMNRRP ILTIITLEDS SGNLLGRNSF EVRVCACPGR DRRTEEENLR KKGEPHHELP PGSTKRALPN NTSSSPQPKK KPLDGEYFTL QIRGRERFEM FRELNEALEL KDAQAGKEPG GSRAHSSHLK SKKGQSTSRH KKLMFKTEGP DSD

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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

Concentration0.02 mg/mL
BufferpH: 7.2 / Component - Name: HEPES buffer
Details: 20 mM HEPES, pH 7.2, 150 mM NaCl, 10 mM CaCl2, 10 mM MgCl2
StainingType: NEGATIVE / Material: Uranyl Formate / Details: 1% uranyl formate
GridSupport film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unspecified

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus min: -1.5 µm / Nominal magnification: 68000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI EAGLE (2k x 2k) / Digitization - Sampling interval: 30.0 µm / Number grids imaged: 1 / Number real images: 20 / Average electron dose: 5.0 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 704
CTF correctionSoftware - Name: RELION (ver. 1.3b)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2ac0


Details: Resolution filtered to ~50 Angstrom
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.3b) / Details: Empirical Bayesian approach
Final 3D classificationNumber classes: 1 / Avg.num./class: 704 / Software - Name: RELION (ver. 1.3b)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.3b) / Details: Empirical Bayesian approach
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 1.3b) / Number images used: 704

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