+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41140 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | APC/C-CDH1-UBE2C-Ubiquitin-CyclinB-NTD | |||||||||||||||
Map data | ||||||||||||||||
Sample |
| |||||||||||||||
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 / positive regulation of exit from mitosis / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / Depolymerization of the Nuclear Lamina / 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 / positive regulation of exit from mitosis / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / Depolymerization of the Nuclear Lamina / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / regulation of mitotic cell cycle spindle assembly checkpoint / free ubiquitin chain polymerization / regulation of meiotic nuclear division / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / 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 / lens fiber cell differentiation / Aberrant regulation of mitotic exit in cancer due to RB1 defects / anaphase-promoting complex-dependent catabolic process / regulation of meiotic cell cycle / positive regulation of mitotic metaphase/anaphase transition / metaphase/anaphase transition of mitotic cell cycle / Nuclear Pore Complex (NPC) Disassembly / (E3-independent) E2 ubiquitin-conjugating enzyme / Transcriptional regulation by RUNX2 / regulation of exit from mitosis / positive regulation of synaptic plasticity / outer kinetochore / Phosphorylation of the APC/C / anaphase-promoting complex binding / mitotic cell cycle phase transition / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / Initiation of Nuclear Envelope (NE) Reformation / exit from mitosis / protein K11-linked ubiquitination / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / enzyme-substrate adaptor activity / cyclin-dependent protein serine/threonine kinase activator activity / Condensation of Prometaphase Chromosomes / regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / ubiquitin-ubiquitin ligase activity / cyclin-dependent protein serine/threonine kinase regulator activity / E2 ubiquitin-conjugating enzyme / mitotic metaphase chromosome alignment / ubiquitin conjugating enzyme activity / ubiquitin-like protein ligase binding / mitotic G2 DNA damage checkpoint signaling / cullin family protein binding / negative regulation of cellular senescence / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin-like ligase-substrate adaptor activity / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / positive regulation of axon extension / heterochromatin / ubiquitin ligase complex / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / Resolution of Sister Chromatid Cohesion / APC/C:Cdc20 mediated degradation of Cyclin B / positive regulation of G2/M transition of mitotic cell cycle / regulation of mitotic cell cycle / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of mitotic cell cycle / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Condensation of Prophase Chromosomes / 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 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / brain development / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / mitotic spindle / spindle / kinetochore / CDK-mediated phosphorylation and removal of Cdc6 / spindle pole / protein polyubiquitination / ubiquitin-protein transferase activity / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / ubiquitin protein ligase activity / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / positive regulation of fibroblast proliferation / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation 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
| |||||||||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_41140.map.gz | 28.4 MB | EMDB map data format | |
---|---|---|---|---|
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 |
-Related structure data
Related structure data | 8tarMC 8tauC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
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) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.13 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_41140_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_41140_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
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 |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.2 µm |
Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 42.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 661289 |