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- PDB-5l9u: Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l9u | ||||||||||||||||||
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Title | Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with a cross linked Ubiquitin variant-substrate-UBE2C (UBCH10) complex representing key features of multiubiquitination | ||||||||||||||||||
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![]() | SIGNALING PROTEIN / ubiquitination / multi-protein complex / cell division | ||||||||||||||||||
Function / homology | ![]() : / : / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / Regulation of FZD by ubiquitination / Regulation of TNFR1 signaling ...: / : / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / Regulation of FZD by ubiquitination / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Fanconi Anemia Pathway / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Cyclin D associated events in G1 / Stabilization of p53 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ER Quality Control Compartment (ERQC) / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / Inactivation of CSF3 (G-CSF) signaling / : / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOD1/2 Signaling Pathway / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / E3 ubiquitin ligases ubiquitinate target proteins / Translesion Synthesis by POLH / Downregulation of ERBB2:ERBB3 signaling / TCF dependent signaling in response to WNT / Regulation of innate immune responses to cytosolic DNA / HDR through Homologous Recombination (HRR) / Downregulation of ERBB2 signaling / Regulation of signaling by CBL / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / NOTCH3 Activation and Transmission of Signal to the Nucleus / protein localization to septin ring / Downregulation of ERBB4 signaling / Stimuli-sensing channels / Deactivation of the beta-catenin transactivating complex / Josephin domain DUBs / Ovarian tumor domain proteases / Negative regulation of MET activity / Interleukin-1 signaling / Regulation of PTEN localization / mitotic morphogenesis checkpoint signaling / Pexophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Metalloprotease DUBs / Regulation of necroptotic cell death / Aggrephagy / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / UCH proteinases / CDK-mediated phosphorylation and removal of Cdc6 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / The role of GTSE1 in G2/M progression after G2 checkpoint / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX3 expression and activity / p75NTR recruits signalling complexes / GLI3 is processed to GLI3R by the proteasome / Activation of NF-kappaB in B cells / Degradation of beta-catenin by the destruction complex / Degradation of AXIN / Regulation of RAS by GAPs / Orc1 removal from chromatin / Neddylation / EGFR downregulation Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.4 Å | ||||||||||||||||||
![]() | Brown, N.G. / VanderLinden, R. / Dube, P. / Haselbach, D. / Peters, J.M. / Stark, H. / Schulman, B.A. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C. Authors: Nicholas G Brown / Ryan VanderLinden / Edmond R Watson / Florian Weissmann / Alban Ordureau / Kuen-Phon Wu / Wei Zhang / Shanshan Yu / Peter Y Mercredi / Joseph S Harrison / Iain F Davidson ...Authors: Nicholas G Brown / Ryan VanderLinden / Edmond R Watson / Florian Weissmann / Alban Ordureau / Kuen-Phon Wu / Wei Zhang / Shanshan Yu / Peter Y Mercredi / Joseph S Harrison / Iain F Davidson / Renping Qiao / Ying Lu / Prakash Dube / Michael R Brunner / Christy R R Grace / Darcie J Miller / David Haselbach / Marc A Jarvis / Masaya Yamaguchi / David Yanishevski / Georg Petzold / Sachdev S Sidhu / Brian Kuhlman / Marc W Kirschner / J Wade Harper / Jan-Michael Peters / Holger Stark / Brenda A Schulman / ![]() ![]() ![]() ![]() Abstract: Protein ubiquitination involves E1, E2, and E3 trienzyme cascades. E2 and RING E3 enzymes often collaborate to first prime a substrate with a single ubiquitin (UB) and then achieve different forms of ...Protein ubiquitination involves E1, E2, and E3 trienzyme cascades. E2 and RING E3 enzymes often collaborate to first prime a substrate with a single ubiquitin (UB) and then achieve different forms of polyubiquitination: multiubiquitination of several sites and elongation of linkage-specific UB chains. Here, cryo-EM and biochemistry show that the human E3 anaphase-promoting complex/cyclosome (APC/C) and its two partner E2s, UBE2C (aka UBCH10) and UBE2S, adopt specialized catalytic architectures for these two distinct forms of polyubiquitination. The APC/C RING constrains UBE2C proximal to a substrate and simultaneously binds a substrate-linked UB to drive processive multiubiquitination. Alternatively, during UB chain elongation, the RING does not bind UBE2S but rather lures an evolving substrate-linked UB to UBE2S positioned through a cullin interaction to generate a Lys11-linked chain. Our findings define mechanisms of APC/C regulation, and establish principles by which specialized E3-E2-substrate-UB architectures control different forms of polyubiquitination. | ||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 366.4 KB | Display | ![]() |
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PDB format | ![]() | 203.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 961.6 KB | Display | ![]() |
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Full document | ![]() | 961.9 KB | Display | |
Data in XML | ![]() | 88.5 KB | Display | |
Data in CIF | ![]() | 136.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3432MC ![]() 3433C ![]() 5jg6C ![]() 5l9tC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Anaphase-promoting complex subunit ... , 11 types, 13 molecules ABDEGWILMNOXY
#1: Protein | Mass: 216725.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||||||||||
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#2: Protein | Mass: 9854.647 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||||||||||
#4: Protein | Mass: 14286.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||||||||||
#5: Protein | Mass: 11677.995 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||||||||||
#7: Protein | Mass: 9793.999 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #8: Protein | | Mass: 93207.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Construct contains the remnant of PreScission Protease site at C-terminus. Source: (gene. exp.) ![]() ![]() #10: Protein | | Mass: 21282.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #11: Protein | | Mass: 8528.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #12: Protein | | Mass: 93938.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #13: Protein | | Mass: 85179.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #17: Protein | Mass: 63204.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Cell division cycle protein ... , 3 types, 6 molecules CPFHJK
#3: Protein | Mass: 68921.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #6: Protein | Mass: 91973.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #9: Protein | Mass: 71747.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Protein , 3 types, 3 molecules RSU
#14: Protein | Mass: 54838.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#15: Protein | Mass: 17057.281 Da / Num. of mol.: 1 / Mutation: K788C,K788C,K788C Source method: isolated from a genetically manipulated source Details: This construct comprises 768-842 of HSL1 with an N-terminal Gemini-IM motif and linker and a C-terminal UB variant (CHAIN V). K788C of this construct is cross-linked to UBE2C C115 (CHAIN U) ...Details: This construct comprises 768-842 of HSL1 with an N-terminal Gemini-IM motif and linker and a C-terminal UB variant (CHAIN V). K788C of this construct is cross-linked to UBE2C C115 (CHAIN U) and to UbG75C (not visible) via TMEA. Source: (gene. exp.) ![]() ![]() ![]() ![]() Gene: HSL1, YKL101W, YKL453 / Production host: ![]() ![]() References: UniProt: P34244, UniProt: Q63429, non-specific serine/threonine protein kinase |
#16: Protein | Mass: 20768.289 Da / Num. of mol.: 1 / Mutation: C102A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: O00762, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Multi-protein complex of APC/C, coactivator CDH1, and cross-linked complex of UBE2C, Ubiquitin, and Substrate-UB_variant fusion. Type: COMPLEX / Entity ID: all |
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Molecular weight | Value: 1.28 MDa / Experimental value: NO |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
EM software | Name: RELION / Version: 1.2 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135578 / Symmetry type: POINT |