+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3463 | |||||||||
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Title | BRCA1-A histone deubiquitinase core complex | |||||||||
Map data | BRCA1-A histone deubiquitinase core complex | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 24.8 Å | |||||||||
Authors | Smerdon SJ / Rosenthal PB | |||||||||
Citation | Journal: Cell Rep / Year: 2016 Title: Three-Dimensional Architecture of the Human BRCA1-A Histone Deubiquitinase Core Complex. Authors: Otto J P Kyrieleis / Pauline B McIntosh / Sarah R Webb / Lesley J Calder / Janette Lloyd / Nisha A Patel / Stephen R Martin / Carol V Robinson / Peter B Rosenthal / Stephen J Smerdon / Abstract: BRCA1 is a tumor suppressor found to be mutated in hereditary breast and ovarian cancer and plays key roles in the maintenance of genomic stability by homologous recombination repair. It is recruited ...BRCA1 is a tumor suppressor found to be mutated in hereditary breast and ovarian cancer and plays key roles in the maintenance of genomic stability by homologous recombination repair. It is recruited to damaged chromatin as a component of the BRCA1-A deubiquitinase, which cleaves K63-linked ubiquitin chains attached to histone H2A and H2AX. BRCA1-A contributes to checkpoint regulation, repair pathway choice, and HR repair efficiency through molecular mechanisms that remain largely obscure. The structure of an active core complex comprising two Abraxas/BRCC36/BRCC45/MERIT40 tetramers determined by negative-stain electron microscopy (EM) reveals a distorted V-shape architecture in which a dimer of Abraxas/BRCC36 heterodimers sits at the base, with BRCC45/Merit40 pairs occupying each arm. The location and ubiquitin-binding activity of BRCC45 suggest that it may provide accessory interactions with nucleosome-linked ubiquitin chains that contribute to their efficient processing. Our data also suggest how ataxia telangiectasia mutated (ATM)-dependent BRCA1 dimerization may stabilize self-association of the entire BRCA1-A complex. | |||||||||
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_3463.map.gz | 2.7 MB | EMDB map data format | |
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Header (meta data) | emd-3463-v30.xml emd-3463.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_3463.png | 50.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3463 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3463 | HTTPS FTP |
-Validation report
Summary document | emd_3463_validation.pdf.gz | 205.6 KB | Display | EMDB validaton report |
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Full document | emd_3463_full_validation.pdf.gz | 204.8 KB | Display | |
Data in XML | emd_3463_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3463 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3463 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3463.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | BRCA1-A histone deubiquitinase core complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.3 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 : BRCA1-A histone deubiquitinase core complex
Entire | Name: BRCA1-A histone deubiquitinase core complex |
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Components |
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-Supramolecule #1: BRCA1-A histone deubiquitinase core complex
Supramolecule | Name: BRCA1-A histone deubiquitinase core complex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET-Duet |
Molecular weight | Experimental: 600 KDa |
-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: 7.5 |
Staining | Type: NEGATIVE / Material: 1% phosphotungstate |
Grid | Model: TAAB / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: FEI EAGLE (2k x 2k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Digitization - Sampling interval: 30.0 µm / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 24.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 8393 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: IMAGIC |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: FREALIGN |
Final 3D classification | Number classes: 30 |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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