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Yorodumi- EMDB-10516: Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10516 | |||||||||
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Title | Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the Mitotic checkpoint complex (APC/C-MCC) at 3.8 angstrom resolution | |||||||||
Map data | Overall map | |||||||||
Sample |
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Keywords | E3 ligase / Complex / Mitotic checkpoint complex / CELL CYCLE | |||||||||
Function / homology | Function and homology information metaphase/anaphase transition of cell cycle / mitotic spindle assembly checkpoint MAD1-MAD2 complex / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic cell cycle spindle assembly checkpoint / regulation of meiotic nuclear division / establishment of centrosome localization / meiotic sister chromatid cohesion, centromeric ...metaphase/anaphase transition of cell cycle / mitotic spindle assembly checkpoint MAD1-MAD2 complex / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic cell cycle spindle assembly checkpoint / regulation of meiotic nuclear division / establishment of centrosome localization / meiotic sister chromatid cohesion, centromeric / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / protein branched polyubiquitination / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / metaphase/anaphase transition of mitotic cell cycle / positive regulation of synaptic plasticity / regulation of exit from mitosis / anaphase-promoting complex binding / Phosphorylation of the APC/C / nuclear pore nuclear basket / outer kinetochore / protein localization to chromosome, centromeric region / positive regulation of mitotic metaphase/anaphase transition / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / positive regulation of dendrite morphogenesis / regulation of mitotic metaphase/anaphase transition / ubiquitin-ubiquitin ligase activity / negative regulation of ubiquitin protein ligase activity / mitotic sister chromatid cohesion / mitotic metaphase chromosome alignment / mitotic spindle assembly checkpoint signaling / establishment of mitotic spindle orientation / Regulation of APC/C activators between G1/S and early anaphase / mitotic sister chromatid segregation / cullin family protein binding / Transcriptional Regulation by VENTX / negative regulation of mitotic cell cycle / mitotic spindle assembly / ubiquitin-like ligase-substrate adaptor activity / positive regulation of axon extension / protein K48-linked ubiquitination / heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / RHO GTPases Activate Formins / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / brain development / negative regulation of protein catabolic process / mitotic spindle / CDK-mediated phosphorylation and removal of Cdc6 / kinetochore / spindle pole / spindle / ubiquitin-protein transferase activity / Separation of Sister Chromatids / microtubule cytoskeleton / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / nervous system development / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein phosphatase binding / molecular adaptor activity / cell differentiation / non-specific serine/threonine protein kinase / protein kinase activity / Ub-specific processing proteases / protein ubiquitination / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleolus / apoptotic process / perinuclear region of cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Alfieri C / Barford D | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: EMBO Rep / Year: 2020 Title: A unique binding mode of Nek2A to the APC/C allows its ubiquitination during prometaphase. Authors: Claudio Alfieri / Thomas Tischer / David Barford / Abstract: The anaphase-promoting complex (APC/C) is the key E3 ubiquitin ligase which directs mitotic progression and exit by catalysing the sequential ubiquitination of specific substrates. The activity of ...The anaphase-promoting complex (APC/C) is the key E3 ubiquitin ligase which directs mitotic progression and exit by catalysing the sequential ubiquitination of specific substrates. The activity of the APC/C in mitosis is restrained by the spindle assembly checkpoint (SAC), which coordinates chromosome segregation with the assembly of the mitotic spindle. The SAC effector is the mitotic checkpoint complex (MCC), which binds and inhibits the APC/C. It is incompletely understood how the APC/C switches substrate specificity in a cell cycle-specific manner. For instance, it is unclear how in prometaphase, when APC/C activity towards cyclin B and securin is repressed by the MCC, the kinase Nek2A is ubiquitinated. Here, we combine biochemical and structural analysis with functional studies in cells to show that Nek2A is a conformational-specific binder of the APC/C-MCC complex (APC/C ) and that, in contrast to cyclin A, Nek2A can be ubiquitinated efficiently by the APC/C in conjunction with both the E2 enzymes UbcH10 and UbcH5. We propose that these special features of Nek2A allow its prometaphase-specific ubiquitination. | |||||||||
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_10516.map.gz | 8.1 MB | EMDB map data format | |
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Header (meta data) | emd-10516-v30.xml emd-10516.xml | 42.1 KB 42.1 KB | Display Display | EMDB header |
Images | emd_10516.png | 70.3 KB | ||
Filedesc metadata | emd-10516.cif.gz | 12.1 KB | ||
Others | emd_10516_additional_1.map.gz emd_10516_additional_2.map.gz emd_10516_additional_3.map.gz | 6 MB 7.1 MB 6.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10516 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10516 | HTTPS FTP |
-Validation report
Summary document | emd_10516_validation.pdf.gz | 429.2 KB | Display | EMDB validaton report |
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Full document | emd_10516_full_validation.pdf.gz | 428.7 KB | Display | |
Data in XML | emd_10516_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_10516_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10516 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10516 | HTTPS FTP |
-Related structure data
Related structure data | 6tljMC 6tm5C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10516.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Overall map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Platform body
File | emd_10516_additional_1.map | ||||||||||||
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Annotation | Platform body | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: TPRlobe body
File | emd_10516_additional_2.map | ||||||||||||
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Annotation | TPRlobe body | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: PC repeats cdc20 and mcc body
File | emd_10516_additional_3.map | ||||||||||||
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Annotation | PC repeats cdc20 and mcc body | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Anaphase-promoting complex/Cyclosome, in complex with the Mitotic...
+Supramolecule #1: Anaphase-promoting complex/Cyclosome, in complex with the Mitotic...
+Macromolecule #1: Anaphase-promoting complex subunit 1
+Macromolecule #2: Anaphase-promoting complex subunit 11
+Macromolecule #3: Cell division cycle protein 23 homolog
+Macromolecule #4: Anaphase-promoting complex subunit 15
+Macromolecule #5: Anaphase-promoting complex subunit 16
+Macromolecule #6: Cell division cycle protein 27 homolog
+Macromolecule #7: Anaphase-promoting complex subunit CDC26
+Macromolecule #8: Anaphase-promoting complex subunit 4
+Macromolecule #9: Cell division cycle protein 16 homolog
+Macromolecule #10: Anaphase-promoting complex subunit 10
+Macromolecule #11: Anaphase-promoting complex subunit 13
+Macromolecule #12: Anaphase-promoting complex subunit 2
+Macromolecule #13: Anaphase-promoting complex subunit 5
+Macromolecule #14: Cell division cycle protein 20 homolog
+Macromolecule #15: Cell division cycle protein 20 homolog
+Macromolecule #16: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta
+Macromolecule #17: Anaphase-promoting complex subunit 7
+Macromolecule #18: Mitotic spindle assembly checkpoint protein MAD2A
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 27.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 343551 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |