+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8926 | |||||||||
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Title | Mutated p53-DNA assembly | |||||||||
Map data | p53 tetramer assembly | |||||||||
Sample |
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Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 15.5 Å | |||||||||
Authors | Kelly DF / Dearnaley WJ / Liang Y | |||||||||
Citation | Journal: 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 |
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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_8926.map.gz | 112.2 KB | EMDB map data format | |
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Header (meta data) | emd-8926-v30.xml emd-8926.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
Images | emd_8926.png | 86.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8926 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8926 | HTTPS FTP |
-Validation report
Summary document | emd_8926_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_8926_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_8926_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8926 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8926 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8926.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | p53 tetramer assembly | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.4 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 : Mutated p53-DNA assembly
Entire | Name: Mutated p53-DNA assembly |
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Components |
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-Supramolecule #1: Mutated p53-DNA assembly
Supramolecule | Name: Mutated p53-DNA assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) / Tissue: Breast |
Molecular weight | Theoretical: 220 KDa |
-Macromolecule #1: Mutated p53-DNA assembly
Macromolecule | Name: Mutated p53-DNA assembly / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: Human (human) / Tissue: Breast |
Sequence | String: 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 PGSTKR |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.2 / Component - Name: HEPES buffer Details: 20 mM HEPES, pH 7.2, 150 mM NaCl, 10 mM CaCl2, 10 mM MgCl2 |
Staining | Type: NEGATIVE / Material: Uranyl Formate / Details: 1% uranyl formate |
Grid | Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026 kPa Details: Grid was coated with amyl acetate followed by a layer of carbon prior to glow discharge. |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: FEI EAGLE (2k x 2k) / Digitization - Sampling interval: 30.0 µm / Number grids imaged: 1 / Number real images: 92 / Average electron dose: 5.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus min: -1.5 µm / Nominal magnification: 68000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |