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Yorodumi- EMDB-8141: Cryo-EM structure of the human FANCD2/FANCI complex reveals a nov... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8141 | |||||||||
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Title | Cryo-EM structure of the human FANCD2/FANCI complex reveals a novel Tower domain required for FANCD2 monoubiquitination- Full length FANCD2/FANCI | |||||||||
Map data | None | |||||||||
Sample |
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Biological species | Helenium autumnale (sneezeweed) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 22.0 Å | |||||||||
Authors | Liang CC / Li Z / Nicholson WV / Venien-Bryan C / Cohn MA | |||||||||
Citation | Journal: Nat Commun / Year: 2016 Title: The FANCD2-FANCI complex is recruited to DNA interstrand crosslinks before monoubiquitination of FANCD2. Authors: Chih-Chao Liang / Zhuolun Li / David Lopez-Martinez / William V Nicholson / Catherine Vénien-Bryan / Martin A Cohn / Abstract: The Fanconi anaemia (FA) pathway is important for the repair of DNA interstrand crosslinks (ICL). The FANCD2-FANCI complex is central to the pathway, and localizes to ICLs dependent on its ...The Fanconi anaemia (FA) pathway is important for the repair of DNA interstrand crosslinks (ICL). The FANCD2-FANCI complex is central to the pathway, and localizes to ICLs dependent on its monoubiquitination. It has remained elusive whether the complex is recruited before or after the critical monoubiquitination. Here, we report the first structural insight into the human FANCD2-FANCI complex by obtaining the cryo-EM structure. The complex contains an inner cavity, large enough to accommodate a double-stranded DNA helix, as well as a protruding Tower domain. Disease-causing mutations in the Tower domain are observed in several FA patients. Our work reveals that recruitment of the complex to a stalled replication fork serves as the trigger for the activating monoubiquitination event. Taken together, our results uncover the mechanism of how the FANCD2-FANCI complex activates the FA pathway, and explains the underlying molecular defect in FA patients with mutations in the Tower domain. | |||||||||
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_8141.map.gz | 374.1 KB | EMDB map data format | |
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Header (meta data) | emd-8141-v30.xml emd-8141.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
Images | emd_8141.png | 42.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8141 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8141 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8141.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.5 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 : human FANCD2/FANCI complex
Entire | Name: human FANCD2/FANCI complex |
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Components |
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-Supramolecule #1: human FANCD2/FANCI complex
Supramolecule | Name: human FANCD2/FANCI complex / type: complex / ID: 1 / Parent: 0 Details: FANCD2 is expressed using the pFastBac1 vector (Life Technologies) with an engineered N-terminal Flag-HA tag, and FANCI is expressed using the pFastBac1 vector (Life Technologies) with an ...Details: FANCD2 is expressed using the pFastBac1 vector (Life Technologies) with an engineered N-terminal Flag-HA tag, and FANCI is expressed using the pFastBac1 vector (Life Technologies) with an engineered N-terminal Flag-MBP tag or a N-terminal Flag-HA tag |
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Source (natural) | Organism: Helenium autumnale (sneezeweed) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: hela / Recombinant plasmid: pX459 |
Molecular weight | Experimental: 300 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 8 / Component: (Name: Tris, KCl) |
Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 293 K / Details: manually prepared with an home-made device. |
-Electron microscopy
Microscope | JEOL 2100 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus min: 3.0 µm / Nominal magnification: 40000 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Temperature | Min: 93.0 K |
Image recording | Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 6 / Average exposure time: 1.0 sec. / Average electron dose: 10.0 e/Å2 |
-Image processing
Particle selection | Number selected: 13222 |
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CTF correction | Software - Name: CTFFIND (ver. 3) |
Startup model | Type of model: RANDOM CONICAL TILT / Random conical tilt - Number images: 8164 / Random conical tilt - Tilt angle: 50 degrees Details: No initial model was existing, an initial model was calculated using the random conical tilt method implemented by SPIDER using 8164 particles negatively stained |
Initial angle assignment | Type: NOT APPLICABLE / Software - Name: SPIDER |
Final 3D classification | Number classes: 4 / Software - Name: RELION |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 5058 |