+Open data
-Basic information
Entry | Database: PDB / ID: 8tar | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | APC/C-CDH1-UBE2C-Ubiquitin-CyclinB-NTD | |||||||||||||||
Components |
| |||||||||||||||
Keywords | TRANSFERASE / E3 RING Ligase / Ubiquitin Ligase / LIGASE | |||||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | |||||||||||||||
Authors | Bodrug, T. / Welsh, K.A. / Bolhuis, D.L. / Paulakonis, E. / Martinez-Chacin, R.C. / Liu, B. / Pinkin, N. / Bonacci, T. / Cui, L. / Xu, P. ...Bodrug, T. / Welsh, K.A. / Bolhuis, D.L. / Paulakonis, E. / Martinez-Chacin, R.C. / Liu, B. / Pinkin, N. / Bonacci, T. / Cui, L. / Xu, P. / Roscow, O. / Amann, S.J. / Grishkovskaya, I. / Emanuele, M.J. / Harrison, J.S. / Steimel, J.P. / Hahn, K.M. / Zhang, W. / Zhong, E. / Haselbach, D. / Brown, N.G. | |||||||||||||||
Funding support | United States, Austria, 4items
| |||||||||||||||
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
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8tar.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8tar.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 8tar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/8tar ftp://data.pdbj.org/pub/pdb/validation_reports/ta/8tar | HTTPS FTP |
---|
-Related structure data
Related structure data | 41140MC 8tauC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Anaphase-promoting complex subunit ... , 11 types, 13 molecules ACDGWHILMNOYZ
#1: Protein | Mass: 217566.141 Da / Num. of mol.: 1 Mutation: S202E, S286E, T291E, S313E, T316E, S317E, S334E, S341E, S343E, S355E, S362E, S372E, S377E, T537E, S547E, S555E, S569E, S688E, S699E, S916E, S1347E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H1A4 | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#3: Protein | Mass: 9854.647 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC11, HSPC214 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NYG5 | ||||||||||||||
#4: Protein | Mass: 6556.302 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC15 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P60006 | ||||||||||||||
#5: Protein | Mass: 9920.108 Da / Num. of mol.: 2 / Mutation: S51E, S52E, S82E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC26, ANAPC12, C9orf17 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NHZ8 #6: Protein | | Mass: 6764.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC16, C10orf104, CENP-27 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96DE5 #7: Protein | | Mass: 92303.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC4, APC4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UJX5 #10: Protein | | Mass: 21310.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC10, APC10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UM13 #11: Protein | | Mass: 8528.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC13 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BS18 #12: Protein | | Mass: 94149.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC2, APC2, KIAA1406 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UJX6 #13: Protein | | Mass: 85445.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC5, APC5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UJX4 #17: Protein | Mass: 63204.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC7, APC7 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UJX3 |
-Cell division cycle protein ... , 3 types, 6 molecules JPKSUV
#8: Protein | Mass: 92519.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC27, ANAPC3, D0S1430E, D17S978E / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30260 #9: Protein | Mass: 71929.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC16, ANAPC6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13042 #16: Protein | Mass: 69075.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC23, ANAPC8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UJX2 |
---|
-Protein , 2 types, 2 molecules QR
#14: Protein | Mass: 16346.630 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2C / Production host: Escherichia coli (E. coli) / References: UniProt: O00762 |
---|---|
#15: Protein | Mass: 55253.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FZR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UM11 |
-Protein/peptide / Non-polymers , 2 types, 5 molecules B
#18: Chemical | ChemComp-ZN / #2: Protein/peptide | | Mass: 1284.467 Da / Num. of mol.: 1 / Fragment: NTD (residues 39-50) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNB1, CCNB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14635 |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Anaphase-promoting complex/cyclosome in complex with CHD1, UBE2C, and Cyclin-B Type: COMPLEX / Entity ID: #1-#17 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1500 nm / Nominal defocus min: 200 nm |
Image recording | Electron dose: 42 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 661289 / Symmetry type: POINT |