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Yorodumi- EMDB-3476: Structure of FANCI-FANCD2 hetero-dimer co-expressed with FANCC-FA... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3476 | |||||||||
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Title | Structure of FANCI-FANCD2 hetero-dimer co-expressed with FANCC-FANCE-FANCF proteins. | |||||||||
Map data | 3D Reconstruction by negative stain EM of FANCI-FANCD2 co-expressed with FANCC-FANCE-FANCF. | |||||||||
Sample |
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Method | single particle reconstruction / negative staining / Resolution: 18.3 Å | |||||||||
Authors | Swuec P / Costa A | |||||||||
Citation | Journal: Cell Rep / Year: 2017 Title: The FA Core Complex Contains a Homo-dimeric Catalytic Module for the Symmetric Mono-ubiquitination of FANCI-FANCD2. Authors: Paolo Swuec / Ludovic Renault / Aaron Borg / Fenil Shah / Vincent J Murphy / Sylvie van Twest / Ambrosius P Snijders / Andrew J Deans / Alessandro Costa / Abstract: Activation of the main DNA interstrand crosslink repair pathway in higher eukaryotes requires mono-ubiquitination of FANCI and FANCD2 by FANCL, the E3 ligase subunit of the Fanconi anemia core ...Activation of the main DNA interstrand crosslink repair pathway in higher eukaryotes requires mono-ubiquitination of FANCI and FANCD2 by FANCL, the E3 ligase subunit of the Fanconi anemia core complex. FANCI and FANCD2 form a stable complex; however, the molecular basis of their ubiquitination is ill defined. FANCD2 mono-ubiquitination by FANCL is stimulated by the presence of the FANCB and FAAP100 core complex components, through an unknown mechanism. How FANCI mono-ubiquitination is achieved remains unclear. Here, we use structural electron microscopy, combined with crosslink-coupled mass spectrometry, to find that FANCB, FANCL, and FAAP100 form a dimer of trimers, containing two FANCL molecules that are ideally poised to target both FANCI and FANCD2 for mono-ubiquitination. The FANCC-FANCE-FANCF subunits bridge between FANCB-FANCL-FAAP100 and the FANCI-FANCD2 substrate. A transient interaction with FANCC-FANCE-FANCF alters the FANCI-FANCD2 configuration, stabilizing the dimerization interface. Our data provide a model to explain how equivalent mono-ubiquitination of FANCI and FANCD2 occurs. | |||||||||
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_3476.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-3476-v30.xml emd-3476.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
Images | emd_3476.png | 39.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3476 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3476 | HTTPS FTP |
-Validation report
Summary document | emd_3476_validation.pdf.gz | 189.2 KB | Display | EMDB validaton report |
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Full document | emd_3476_full_validation.pdf.gz | 188.3 KB | Display | |
Data in XML | emd_3476_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3476 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3476 | 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_3476.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D Reconstruction by negative stain EM of FANCI-FANCD2 co-expressed with FANCC-FANCE-FANCF. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.7 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 : Hetero-dimeric complex of FANCI and FANCD2 proteins recombinantly...
Entire | Name: Hetero-dimeric complex of FANCI and FANCD2 proteins recombinantly co-expressed with the FANCC-FANCE-FANCF ternary complex. |
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Components |
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-Supramolecule #1: Hetero-dimeric complex of FANCI and FANCD2 proteins recombinantly...
Supramolecule | Name: Hetero-dimeric complex of FANCI and FANCD2 proteins recombinantly co-expressed with the FANCC-FANCE-FANCF ternary complex. type: complex / ID: 1 / Parent: 0 |
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Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.005 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Staining | Type: NEGATIVE / Material: Uranyl formate Details: The sample stained with a fresh 2% (wt/vol) uranyl formate solution. | ||||||||||||
Grid | Model: 3.05mm diameter, square mesh grids. / Material: COPPER / Mesh: 600 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 4.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR Details: Prior to sample incubation, the carbon-coated grid was glow-discharged for 30 seconds at 45 mA. |
-Electron microscopy
Microscope | JEOL 2100 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 447 / Average electron dose: 35.0 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 max: 2.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: JEOL |