+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15003 | |||||||||||||||
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Title | ARISC-RAP80 complex, Map 5 | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.9 Å | |||||||||||||||
Authors | Foglizzo M / Zeqiraj E | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: J Cell Biol / Year: 2022 Title: Autologous K63 deubiquitylation within the BRCA1-A complex licenses DNA damage recognition. Authors: Qinqin Jiang / Martina Foglizzo / Yaroslav I Morozov / Xuejiao Yang / Arindam Datta / Lei Tian / Vaughn Thada / Weihua Li / Elton Zeqiraj / Roger A Greenberg / Abstract: The BRCA1-A complex contains matching lysine-63 ubiquitin (K63-Ub) binding and deubiquitylating activities. How these functionalities are coordinated to effectively respond to DNA damage remains ...The BRCA1-A complex contains matching lysine-63 ubiquitin (K63-Ub) binding and deubiquitylating activities. How these functionalities are coordinated to effectively respond to DNA damage remains unknown. We generated Brcc36 deubiquitylating enzyme (DUB) inactive mice to address this gap in knowledge in a physiologic system. DUB inactivation impaired BRCA1-A complex damage localization and repair activities while causing early lethality when combined with Brca2 mutation. Damage response dysfunction in DUB-inactive cells corresponded to increased K63-Ub on RAP80 and BRCC36. Chemical cross-linking coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) and cryogenic-electron microscopy (cryo-EM) analyses of isolated BRCA1-A complexes demonstrated the RAP80 ubiquitin interaction motifs are occupied by ubiquitin exclusively in the DUB-inactive complex, linking auto-inhibition by internal K63-Ub chains to loss of damage site ubiquitin recognition. These findings identify RAP80 and BRCC36 as autologous DUB substrates in the BRCA1-A complex, thus explaining the evolution of matching ubiquitin-binding and hydrolysis activities within a single macromolecular assembly. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15003.map.gz | 74.3 MB | EMDB map data format | |
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Header (meta data) | emd-15003-v30.xml emd-15003.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
Images | emd_15003.png | 32.9 KB | ||
Masks | emd_15003_msk_1.map | 125 MB | Mask map | |
Others | emd_15003_half_map_1.map.gz emd_15003_half_map_2.map.gz | 98.2 MB 98.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15003 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15003 | HTTPS FTP |
-Validation report
Summary document | emd_15003_validation.pdf.gz | 621.6 KB | Display | EMDB validaton report |
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Full document | emd_15003_full_validation.pdf.gz | 621.2 KB | Display | |
Data in XML | emd_15003_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | emd_15003_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15003 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15003 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15003.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15003_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15003_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15003_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex containing the four-subunit ARISC together with FL RAP80
Entire | Name: Complex containing the four-subunit ARISC together with FL RAP80 |
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Components |
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-Supramolecule #1: Complex containing the four-subunit ARISC together with FL RAP80
Supramolecule | Name: Complex containing the four-subunit ARISC together with FL RAP80 type: complex / Chimera: Yes / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Experimental: 235 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.16 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: The sample was supplemented with 2 mM EDTA/EGTA mixture immediately before grids preparation | ||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: The sample was blotted for 6 seconds and with a blot force of 6 before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4392 / Average exposure time: 70.0 sec. / Average electron dose: 1.46 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |