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- EMDB-51070: Focused refined map of the Anaphase-promoting complex/cyclosome (... -
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Open data
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Basic information
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Title | Focused refined map of the Anaphase-promoting complex/cyclosome (APC/C) with mask 3 | |||||||||
![]() | Focused refined map (sharpened with deepEMhancer) of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-factor Cdh1 | |||||||||
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![]() | APC/C / cyclosome / Cdc20 / Cdh1 / ubiquitination / Emi1 / mitosis / Cell cycle / LIGASE | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Hoefler A / Yu J / Chang L / Zhang Z / Yang J / Boland A / Barford D | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Cryo-EM structures of apo-APC/C and APC/C complexes provide insights into APC/C regulation. Authors: Anna Höfler / Jun Yu / Jing Yang / Ziguo Zhang / Leifu Chang / Stephen H McLaughlin / Geoffrey W Grime / Elspeth F Garman / Andreas Boland / David Barford / ![]() ![]() Abstract: APC/C is a multi-subunit complex that functions as a master regulator of cell division. It controls progression through the cell cycle by timely marking mitotic cyclins and other cell cycle ...APC/C is a multi-subunit complex that functions as a master regulator of cell division. It controls progression through the cell cycle by timely marking mitotic cyclins and other cell cycle regulatory proteins for degradation. The APC/C itself is regulated by the sequential action of its coactivator subunits CDC20 and CDH1, post-translational modifications, and its inhibitory binding partners EMI1 and the mitotic checkpoint complex. In this study, we took advantage of developments in cryo-electron microscopy to determine the structures of human APC/C and apo-APC/C at 2.9 Å and 3.2 Å resolution, respectively, providing insights into the regulation of APC/C activity. The high-resolution maps allow the unambiguous assignment of an α-helix to the N-terminus of CDH1 (CDH1) in the APC/C ternary complex. We also identify a zinc-binding module in APC2 that confers structural stability to the complex, and we confirm the presence of zinc ions experimentally. Finally, due to the higher resolution and well defined density of these maps, we are able to build, aided by AlphaFold predictions, several intrinsically disordered regions in different APC/C subunits that likely play a role in proper APC/C assembly and regulation of its activity. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 156.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.9 KB 19.9 KB | Display Display | ![]() |
Images | ![]() | 56.9 KB | ||
Filedesc metadata | ![]() | 5 KB | ||
Others | ![]() ![]() ![]() | 88.8 MB 165 MB 165 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 809.1 KB | Display | ![]() |
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Full document | ![]() | 808.7 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | Focused refined map (sharpened with deepEMhancer) of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-factor Cdh1 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Focused refined map (unsharpened) of the Anaphase-promoting complex/cyclosome...
File | emd_51070_additional_1.map | ||||||||||||
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Annotation | Focused refined map (unsharpened) of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-factor Cdh1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A of focused refinement of the...
File | emd_51070_half_map_1.map | ||||||||||||
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Annotation | Half map A of focused refinement of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-factor Cdh1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of focused refinement of the...
File | emd_51070_half_map_2.map | ||||||||||||
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Annotation | Half map B of focused refinement of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-factor Cdh1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
Entire | Name: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1 |
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Components |
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-Supramolecule #1: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
Supramolecule | Name: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.2 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III |
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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 / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 8297 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 2.7 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |