+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41140 | |||||||||||||||
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Title | APC/C-CDH1-UBE2C-Ubiquitin-CyclinB-NTD | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | E3 RING Ligase / Ubiquitin Ligase / LIGASE / TRANSFERASE | |||||||||||||||
Function / homology | Function and homology information cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of anaphase-promoting complex-dependent catabolic process / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / Depolymerization of the Nuclear Lamina / positive regulation of exit from mitosis / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression ...cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of anaphase-promoting complex-dependent catabolic process / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / Depolymerization of the Nuclear Lamina / positive regulation of exit from mitosis / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / free ubiquitin chain polymerization / 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 / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / patched binding / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / lens fiber cell differentiation / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of synaptic plasticity / regulation of exit from mitosis / Nuclear Pore Complex (NPC) Disassembly / Transcriptional regulation by RUNX2 / anaphase-promoting complex binding / outer kinetochore / Phosphorylation of the APC/C / mitotic cell cycle phase transition / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / Initiation of Nuclear Envelope (NE) Reformation / Regulation of APC/C activators between G1/S and early anaphase / Polo-like kinase mediated events / protein K11-linked ubiquitination / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / cyclin-dependent protein serine/threonine kinase activator activity / enzyme-substrate adaptor activity / Condensation of Prometaphase Chromosomes / positive regulation of dendrite morphogenesis / regulation of mitotic metaphase/anaphase transition / cyclin-dependent protein serine/threonine kinase regulator activity / exit from mitosis / ubiquitin-ubiquitin ligase activity / mitotic metaphase chromosome alignment / E2 ubiquitin-conjugating enzyme / positive regulation of G2/M transition of mitotic cell cycle / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / ubiquitin-like protein ligase binding / regulation of mitotic cell cycle / mitotic G2 DNA damage checkpoint signaling / negative regulation of cellular senescence / cullin family protein binding / ubiquitin conjugating enzyme activity / Transcriptional Regulation by VENTX / ubiquitin-like ligase-substrate adaptor activity / positive regulation of axon extension / protein K48-linked ubiquitination / heterochromatin / Nuclear events stimulated by ALK signaling in cancer / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / ubiquitin ligase complex / Resolution of Sister Chromatid Cohesion / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / positive regulation of mitotic cell cycle / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Condensation of Prophase Chromosomes / mitotic spindle organization / nuclear periphery / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / 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 / CDK-mediated phosphorylation and removal of Cdc6 / 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 / mitotic spindle / kinetochore / G2/M transition of mitotic cell cycle / spindle pole / positive regulation of fibroblast proliferation / spindle / protein polyubiquitination / Separation of Sister Chromatids / ubiquitin-protein transferase activity / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||||||||
Authors | Bodrug T / Welsh KA / Bolhuis DL / Paulakonis E / Martinez-Chacin RC / Liu B / Pinkin N / Bonacci T / Cui L / Xu P ...Bodrug T / Welsh KA / Bolhuis DL / Paulakonis E / Martinez-Chacin RC / Liu B / Pinkin N / Bonacci T / Cui L / Xu P / Roscow O / Amann SJ / Grishkovskaya I / Emanuele MJ / Harrison JS / Steimel JP / Hahn KM / Zhang W / Zhong E / Haselbach D / Brown NG | |||||||||||||||
Funding support | United States, Austria, 4 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Time-resolved cryo-EM (TR-EM) analysis of substrate polyubiquitination by the RING E3 anaphase-promoting complex/cyclosome (APC/C). Authors: Tatyana Bodrug / Kaeli A Welsh / Derek L Bolhuis / Ethan Paulаkonis / Raquel C Martinez-Chacin / Bei Liu / Nicholas Pinkin / Thomas Bonacci / Liying Cui / Pengning Xu / Olivia Roscow / ...Authors: Tatyana Bodrug / Kaeli A Welsh / Derek L Bolhuis / Ethan Paulаkonis / Raquel C Martinez-Chacin / Bei Liu / Nicholas Pinkin / Thomas Bonacci / Liying Cui / Pengning Xu / Olivia Roscow / Sascha Josef Amann / Irina Grishkovskaya / Michael J Emanuele / Joseph S Harrison / Joshua P Steimel / Klaus M Hahn / Wei Zhang / Ellen D Zhong / David Haselbach / Nicholas G Brown / Abstract: Substrate polyubiquitination drives a myriad of cellular processes, including the cell cycle, apoptosis and immune responses. Polyubiquitination is highly dynamic, and obtaining mechanistic insight ...Substrate polyubiquitination drives a myriad of cellular processes, including the cell cycle, apoptosis and immune responses. Polyubiquitination is highly dynamic, and obtaining mechanistic insight has thus far required artificially trapped structures to stabilize specific steps along the enzymatic process. So far, how any ubiquitin ligase builds a proteasomal degradation signal, which is canonically regarded as four or more ubiquitins, remains unclear. Here we present time-resolved cryogenic electron microscopy studies of the 1.2 MDa E3 ubiquitin ligase, known as the anaphase-promoting complex/cyclosome (APC/C), and its E2 co-enzymes (UBE2C/UBCH10 and UBE2S) during substrate polyubiquitination. Using cryoDRGN (Deep Reconstructing Generative Networks), a neural network-based approach, we reconstruct the conformational changes undergone by the human APC/C during polyubiquitination, directly visualize an active E3-E2 pair modifying its substrate, and identify unexpected interactions between multiple ubiquitins with parts of the APC/C machinery, including its coactivator CDH1. Together, we demonstrate how modification of substrates with nascent ubiquitin chains helps to potentiate processive substrate polyubiquitination, allowing us to model how a ubiquitin ligase builds a proteasomal degradation signal. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41140.map.gz | 28.4 MB | EMDB map data format | |
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Header (meta data) | emd-41140-v30.xml emd-41140.xml | 40.6 KB 40.6 KB | Display Display | EMDB header |
Images | emd_41140.png | 82.5 KB | ||
Filedesc metadata | emd-41140.cif.gz | 12.1 KB | ||
Others | emd_41140_half_map_1.map.gz emd_41140_half_map_2.map.gz | 226.5 MB 226.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41140 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41140 | HTTPS FTP |
-Validation report
Summary document | emd_41140_validation.pdf.gz | 760 KB | Display | EMDB validaton report |
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Full document | emd_41140_full_validation.pdf.gz | 759.6 KB | Display | |
Data in XML | emd_41140_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_41140_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41140 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41140 | HTTPS FTP |
-Related structure data
Related structure data | 8tarMC 8tauC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41140.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.13 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41140_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41140_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Anaphase-promoting complex/cyclosome in complex with CHD1, UBE2C,...
+Supramolecule #1: Anaphase-promoting complex/cyclosome in complex with CHD1, UBE2C,...
+Macromolecule #1: Anaphase-promoting complex subunit 1
+Macromolecule #2: G2/mitotic-specific cyclin-B1
+Macromolecule #3: Anaphase-promoting complex subunit 11
+Macromolecule #4: Anaphase-promoting complex subunit 15
+Macromolecule #5: Anaphase-promoting complex subunit CDC26
+Macromolecule #6: Anaphase-promoting complex subunit 16
+Macromolecule #7: Anaphase-promoting complex subunit 4
+Macromolecule #8: Cell division cycle protein 27 homolog
+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: Ubiquitin-conjugating enzyme E2 C
+Macromolecule #15: Fizzy-related protein homolog
+Macromolecule #16: Cell division cycle protein 23 homolog
+Macromolecule #17: Anaphase-promoting complex subunit 7
+Macromolecule #18: ZINC ION
-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 TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 661289 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |