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- EMDB-3433: Anaphase-promoting complex/Cyclosome (APC/C)-CDH1-UBE2S-Ubiquitin... -

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Entry
Database: EMDB / ID: EMD-3433
TitleAnaphase-promoting complex/Cyclosome (APC/C)-CDH1-UBE2S-Ubiquitin (variant)-substrate
Map dataAnaphase-promoting complex/Cyclosome (APC/C)-CDH1-UBE2S-Ubiquitin (variant)-substrate
Sample
  • Sample: Anaphase-promoting complex/Cyclosome (APC/C)-CDH1-UBE2S-Ubiquitin (variant)-substrate
  • Protein or peptide: Anaphase Promoting ComplexAnaphase-promoting complex
KeywordsAnaphase Promoting Complex / ubiquitin ligation
Function / homology
Function and homology information


protein localization to septin ring / mitotic morphogenesis checkpoint signaling / cellular bud neck septin ring / positive regulation of anaphase-promoting complex-dependent catabolic process / protein K29-linked ubiquitination / protein K27-linked ubiquitination / regulation of mitotic cell cycle spindle assembly checkpoint / free ubiquitin chain polymerization / regulation of meiotic nuclear division / positive regulation of synapse maturation ...protein localization to septin ring / mitotic morphogenesis checkpoint signaling / cellular bud neck septin ring / positive regulation of anaphase-promoting complex-dependent catabolic process / protein K29-linked ubiquitination / protein K27-linked ubiquitination / 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 / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / 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 / regulation of exit from mitosis / positive regulation of synaptic plasticity / Phosphorylation of the APC/C / anaphase-promoting complex binding / protein K6-linked ubiquitination / cellular bud neck / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / exit from mitosis / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / hypothalamus gonadotrophin-releasing hormone neuron development / regulation of mitotic metaphase/anaphase transition / female meiosis I / positive regulation of dendrite morphogenesis / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / fat pad development / mitotic metaphase chromosome alignment / female gonad development / seminiferous tubule development / male meiosis I / ubiquitin conjugating enzyme activity / regulation of mitotic cell cycle / protein K63-linked ubiquitination / negative regulation of cellular senescence / mitotic G2 DNA damage checkpoint signaling / cullin family protein binding / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin-like ligase-substrate adaptor activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional Regulation by VENTX / positive regulation of axon extension / regulation of proteasomal protein catabolic process / heterochromatin / energy homeostasis / regulation of neuron apoptotic process / Cyclin A:Cdk2-associated events at S phase entry / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK
Similarity search - Function
Anaphase-promoting complex subunit 15 / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 4, metazoa / : / Anaphase-promoting complex subunit 5, N-terminal domain / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain / : / : ...Anaphase-promoting complex subunit 15 / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 4, metazoa / : / Anaphase-promoting complex subunit 5, N-terminal domain / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain / : / : / Anaphase-promoting complex subunit 1 WD40 beta-propeller domain / Anaphase-promoting complex sub unit 1 C-terminal domain / Anaphase-promoting complex subunit 1 middle domain / APC1 beta sandwich domain / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex, subunit 16 / Cdc23 / Apc13 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 4 long domain / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein / Anaphase-promoting complex, cyclosome, subunit 4 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 5 domain / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit APC10/Doc1 / Anaphase-promoting complex, subunit CDC26 / Anaphase-promoting complex APC subunit CDC26 / Anaphase-promoting complex subunit 11, RING-H2 finger / Anaphase-promoting complex subunit 11 RING-H2 finger / Anaphase-promoting complex subunit 2, C-terminal / Anaphase-promoting complex subunit 2 / Anaphase promoting complex (APC) subunit 2 / Anaphase promoting complex (APC) subunit 2 / Anaphase-promoting complex, cyclosome, subunit 3 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / TPR repeat / Tetratricopeptide repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Tetratricopeptide repeat / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Ubiquitin conserved site / Ubiquitin domain / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin domain signature. / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Tetratricopeptide-like helical domain superfamily / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / Cell division cycle protein 27 homolog / Probable serine/threonine-protein kinase HSL1 / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / Ubiquitin-conjugating enzyme E2 S / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit 1 ...Polyubiquitin-B / Cell division cycle protein 27 homolog / Probable serine/threonine-protein kinase HSL1 / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / Ubiquitin-conjugating enzyme E2 S / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 11 / Cell division cycle protein 23 homolog / Anaphase-promoting complex subunit 7 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 2 / Fizzy-related protein homolog / Anaphase-promoting complex subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsBrown N / VanderLinden R / Watson E / Weissmann F / Ordureau A / Wu K-P / Yu S / Mercedi P / Harrison J / Davidson I ...Brown N / VanderLinden R / Watson E / Weissmann F / Ordureau A / Wu K-P / Yu S / Mercedi P / Harrison J / Davidson I / Coudevylle R / Lu Y / Dube P / Brunner M / Grace CRR / Miller D / Haselbach D / Jarvis M / Yamaguchi M / Yanishevski D / Petzold G / Sidhu S / Kuhlman B / Kirschner M / Harper JW / Peters J-M / Stark H / Schulman BA
CitationJournal: Cell / Year: 2016
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
DepositionMay 10, 2016-
Header (metadata) releaseJun 15, 2016-
Map releaseJul 20, 2016-
UpdateNov 2, 2016-
Current statusNov 2, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5l9t
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

image_3433.png

Downloads & links

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Map

FileDownload / File: emd_3433.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAnaphase-promoting complex/Cyclosome (APC/C)-CDH1-UBE2S-Ubiquitin (variant)-substrate
Voxel sizeX=Y=Z: 1.57 Å
Density
Contour LevelBy AUTHOR: 0.065 / Movie #1: 0.065
Minimum - Maximum-0.08904973 - 0.2057582
Average (Standard dev.)0.0002983 (±0.01344598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 401.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.571.571.57
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z401.920401.920401.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0890.2060.000

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Supplemental data

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Sample components

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Entire : Anaphase-promoting complex/Cyclosome (APC/C)-CDH1-UBE2S-Ubiquitin...

EntireName: Anaphase-promoting complex/Cyclosome (APC/C)-CDH1-UBE2S-Ubiquitin (variant)-substrate
Components
  • Sample: Anaphase-promoting complex/Cyclosome (APC/C)-CDH1-UBE2S-Ubiquitin (variant)-substrate
  • Protein or peptide: Anaphase Promoting ComplexAnaphase-promoting complex

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Supramolecule #1000: Anaphase-promoting complex/Cyclosome (APC/C)-CDH1-UBE2S-Ubiquitin...

SupramoleculeName: Anaphase-promoting complex/Cyclosome (APC/C)-CDH1-UBE2S-Ubiquitin (variant)-substrate
type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 1.5 MDa

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Macromolecule #1: Anaphase Promoting Complex

MacromoleculeName: Anaphase Promoting Complex / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8 / Details: 50 mM Hepes, 150 mM NaCl, 2 mM MgCl2
GridDetails: 200 mesh copper grids, quantifoil with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 89000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.0001 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.7 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateJul 31, 2015
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 2070 / Average electron dose: 40 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER / Number images used: 125390

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