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Yorodumi- EMDB-4465: Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4465 | |||||||||
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Title | Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D1 box class | |||||||||
Map data | unsharpened map | |||||||||
Sample |
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Keywords | spindle assembly checkpoint / anaphase-promoting complex / cyclin / ubiquitination / CELL CYCLE | |||||||||
Function / homology | Function and homology information metaphase/anaphase transition of cell cycle / 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 / regulation of meiotic nuclear division / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of synapse maturation / Inactivation of APC/C via direct inhibition of the APC/C complex ...metaphase/anaphase transition of cell cycle / 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 / regulation of meiotic nuclear division / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of synapse maturation / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / G2 Phase / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / Phosphorylation of Emi1 / cyclin A2-CDK1 complex / cyclin A2-CDK2 complex / anaphase-promoting complex / cell cycle G1/S phase transition / Aberrant regulation of mitotic exit in cancer due to RB1 defects / cellular response to luteinizing hormone stimulus / p53-Dependent G1 DNA Damage Response / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / positive regulation of synaptic plasticity / regulation of exit from mitosis / anaphase-promoting complex binding / Phosphorylation of the APC/C / mitotic cell cycle phase transition / positive regulation of mitotic metaphase/anaphase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / Regulation of APC/C activators between G1/S and early anaphase / cellular response to leptin stimulus / protein K11-linked ubiquitination / male pronucleus / Telomere Extension By Telomerase / G0 and Early G1 / female pronucleus / enzyme-substrate adaptor activity / positive regulation of dendrite morphogenesis / response to glucagon / cellular response to cocaine / regulation of mitotic metaphase/anaphase transition / cellular response to nitric oxide / cyclin-dependent protein serine/threonine kinase regulator activity / ubiquitin-ubiquitin ligase activity / cellular response to insulin-like growth factor stimulus / mitotic sister chromatid cohesion / mitotic metaphase chromosome alignment / positive regulation of DNA biosynthetic process / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cochlea development / cellular response to platelet-derived growth factor stimulus / mitotic spindle assembly checkpoint signaling / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / regulation of DNA replication / regulation of mitotic cell cycle / cullin family protein binding / Transcriptional Regulation by VENTX / ubiquitin-like ligase-substrate adaptor activity / mitotic spindle assembly / positive regulation of axon extension / animal organ regeneration / protein K48-linked ubiquitination / post-translational protein modification / heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / cellular response to estradiol stimulus / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / DNA Damage/Telomere Stress Induced Senescence / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Assembly of the pre-replicative complex / RHO GTPases Activate Formins / CDK-mediated phosphorylation and removal of Cdc6 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / brain development / G1/S transition of mitotic cell cycle / mitotic spindle / kinetochore / G2/M transition of mitotic cell cycle / spindle pole / positive regulation of fibroblast proliferation / spindle / Regulation of TP53 Degradation / Separation of Sister Chromatids / ubiquitin-protein transferase activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Zhang S / Barford D | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Cyclin A2 degradation during the spindle assembly checkpoint requires multiple binding modes to the APC/C. Authors: Suyang Zhang / Thomas Tischer / David Barford / Abstract: The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are ...The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are both targeted for degradation by the APC/C, during the spindle assembly checkpoint (SAC), the mitotic checkpoint complex (MCC) represses APC/C's activity towards cyclin B1, but not cyclin A2. Through structural, biochemical and in vivo analysis, we identify a non-canonical D box (D2) that is critical for cyclin A2 ubiquitination in vitro and degradation in vivo. During the SAC, cyclin A2 is ubiquitinated by the repressed APC/C-MCC, mediated by the cooperative engagement of its KEN and D2 boxes, ABBA motif, and the cofactor Cks. Once the SAC is satisfied, cyclin A2 binds APC/C-Cdc20 through two mutually exclusive binding modes, resulting in differential ubiquitination efficiency. Our findings reveal that a single substrate can engage an E3 ligase through multiple binding modes, affecting its degradation timing and efficiency. | |||||||||
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_4465.map.gz | 213.7 MB | EMDB map data format | |
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Header (meta data) | emd-4465-v30.xml emd-4465.xml | 43.8 KB 43.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4465_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_4465.png | 160.8 KB | ||
Filedesc metadata | emd-4465.cif.gz | 12 KB | ||
Others | emd_4465_additional.map.gz emd_4465_half_map_1.map.gz emd_4465_half_map_2.map.gz | 10.2 MB 194.7 MB 194.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4465 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4465 | HTTPS FTP |
-Validation report
Summary document | emd_4465_validation.pdf.gz | 429.8 KB | Display | EMDB validaton report |
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Full document | emd_4465_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | emd_4465_validation.xml.gz | 19.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4465 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4465 | HTTPS FTP |
-Related structure data
Related structure data | 6q6gMC 4463C 4464C 4466C 4467C 6q6hC C: citing same article (ref.) M: atomic model generated by this map |
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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_4465.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | unsharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.047 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: sharpened map with B factor -30 and lowpass filtered to 4A
File | emd_4465_additional.map | ||||||||||||
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Annotation | sharpened map with B factor -30 and lowpass filtered to 4A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap1
File | emd_4465_half_map_1.map | ||||||||||||
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Annotation | halfmap1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap2
File | emd_4465_half_map_2.map | ||||||||||||
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Annotation | halfmap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, ...
+Supramolecule #1: Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, ...
+Supramolecule #2: Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, ...
+Supramolecule #3: Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, ...
+Macromolecule #1: Cell division cycle protein 20 homolog
+Macromolecule #2: Cyclin-A2
+Macromolecule #3: Anaphase-promoting complex subunit 10
+Macromolecule #4: Anaphase-promoting complex subunit 15
+Macromolecule #5: Anaphase-promoting complex subunit 1,Anaphase-promoting complex s...
+Macromolecule #6: Anaphase-promoting complex subunit 2
+Macromolecule #7: Anaphase-promoting complex subunit 4
+Macromolecule #8: Anaphase-promoting complex subunit 5
+Macromolecule #9: Cell division cycle protein 16 homolog
+Macromolecule #10: Anaphase-promoting complex subunit 11
+Macromolecule #11: Anaphase-promoting complex subunit CDC26
+Macromolecule #12: Anaphase-promoting complex subunit 13
+Macromolecule #13: Anaphase-promoting complex subunit 16
+Macromolecule #14: Cell division cycle protein 27 homolog
+Macromolecule #15: Anaphase-promoting complex subunit 7
+Macromolecule #16: Cell division cycle protein 23 homolog
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 8 / Details: 20mM Hepes, 150mM NaCl, 0.5mM TCEP |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 28.0 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: Titan Krios / Image courtesy: FEI Company |