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Entry
Database: PDB / ID: 7qe7
TitleHigh-resolution structure of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-activator Cdh1
Components
  • (Anaphase-promoting complex subunit ...) x 11
  • (Cell division cycle protein ...Cell cycle) x 3
  • F-box only protein 5
  • Fizzy-related protein homolog
KeywordsCELL CYCLE / APC/C / cyclosome / Cdc20 / Cdh1 / ubiquitination / Emi1 / mitosis
Function / homology
Function and homology information


negative regulation of DNA endoreduplication / negative regulation of mitotic metaphase/anaphase transition / negative regulation of meiotic nuclear division / positive regulation of biomineral tissue development / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of mesenchymal stem cell migration / regulation of mitotic cell cycle spindle assembly checkpoint / Mitotic Metaphase/Anaphase Transition / regulation of meiotic nuclear division / positive regulation of synapse maturation ...negative regulation of DNA endoreduplication / negative regulation of mitotic metaphase/anaphase transition / negative regulation of meiotic nuclear division / positive regulation of biomineral tissue development / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of mesenchymal stem cell migration / regulation of mitotic cell cycle spindle assembly checkpoint / Mitotic Metaphase/Anaphase Transition / regulation of meiotic nuclear division / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / vesicle organization / 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 / negative regulation of ubiquitin-protein transferase activity / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / oocyte maturation / spindle assembly involved in female meiosis I / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / meiotic spindle / regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / ubiquitin-ubiquitin ligase activity / ubiquitin ligase inhibitor activity / negative regulation of ubiquitin protein ligase activity / regulation of mitotic nuclear division / mitotic metaphase chromosome alignment / G1/S-Specific Transcription / molecular function inhibitor activity / microtubule polymerization / regulation of mitotic cell cycle / cullin family protein binding / negative regulation of cellular senescence / mitotic G2 DNA damage checkpoint signaling / regulation of DNA replication / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin-like ligase-substrate adaptor activity / Transcriptional Regulation by VENTX / positive regulation of axon extension / positive regulation of osteoblast differentiation / heterochromatin / Cyclin A:Cdk2-associated events at S phase entry / APC/C:Cdc20 mediated degradation of Cyclin B / positive regulation of G2/M transition of mitotic cell cycle / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / 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 / spindle / mitotic spindle / kinetochore / CDK-mediated phosphorylation and removal of Cdc6 / ubiquitin-protein transferase activity / Separation of Sister Chromatids / ubiquitin protein ligase activity / microtubule cytoskeleton / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / nervous system development / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / nuclear membrane / cell differentiation / molecular adaptor activity / protein ubiquitination / cell cycle / cell division / negative regulation of gene expression / DNA repair / centrosome / DNA damage response / ubiquitin protein ligase binding / positive regulation of cell population proliferation / nucleolus / protein kinase binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Zinc finger ZBR-type domain / : / Zinc finger ZBR-type profile. / F-box 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 ...Zinc finger ZBR-type domain / : / Zinc finger ZBR-type profile. / F-box 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 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Anaphase-promoting complex, cyclosome, subunit 3 / TPR repeat / F-box domain / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / WD40 repeat, conserved site / Winged helix DNA-binding domain superfamily / 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 / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / 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 ...Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / 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 / F-box only protein 5 / Fizzy-related protein homolog / Anaphase-promoting complex subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsHoefler, A. / Yu, J. / Chang, L. / Zhang, Z. / Yang, J. / Boland, A. / Barford, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_185235 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/6 United Kingdom
CitationJournal: To Be Published
Title: High-resolution structure of the Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
Authors: Hoefler, A. / Yu, J. / Chang, L. / Zhang, Z. / Yang, J. / Boland, A. / Barford, D.
History
DepositionDec 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
L: Anaphase-promoting complex subunit 10
D: Anaphase-promoting complex subunit 15
A: Anaphase-promoting complex subunit 1
N: Anaphase-promoting complex subunit 2
I: Anaphase-promoting complex subunit 4
O: Anaphase-promoting complex subunit 5
S: F-box only protein 5
K: Cell division cycle protein 16 homolog
G: Anaphase-promoting complex subunit CDC26
W: Anaphase-promoting complex subunit CDC26
M: Anaphase-promoting complex subunit 13
H: Anaphase-promoting complex subunit 16
J: Cell division cycle protein 27 homolog
P: Cell division cycle protein 27 homolog
Q: Cell division cycle protein 16 homolog
Y: Anaphase-promoting complex subunit 7
U: Cell division cycle protein 23 homolog
V: Cell division cycle protein 23 homolog
Z: Anaphase-promoting complex subunit 7
R: Fizzy-related protein homolog
C: Anaphase-promoting complex subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,279,09127
Polymers1,278,69921
Non-polymers3926
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area125060 Å2
ΔGint-589 kcal/mol
Surface area350150 Å2

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Components

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Anaphase-promoting complex subunit ... , 11 types, 13 molecules LDANIOGWMHYZC

#1: Protein Anaphase-promoting complex subunit 10 / / APC10 / Cyclosome subunit 10


Mass: 21282.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC10, APC10 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UM13
#2: Protein Anaphase-promoting complex subunit 15 / / APC15


Mass: 14286.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC15, C11orf51, HSPC020 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60006
#3: Protein Anaphase-promoting complex subunit 1 / / APC1 / Cyclosome subunit 1 / Mitotic checkpoint regulator / Testis-specific gene 24 protein


Mass: 216725.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC1, TSG24 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H1A4
#4: Protein Anaphase-promoting complex subunit 2 / / APC2 / Cyclosome subunit 2


Mass: 93938.977 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX6
#5: Protein Anaphase-promoting complex subunit 4 / / APC4 / Cyclosome subunit 4


Mass: 93014.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC4, APC4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX5
#6: Protein Anaphase-promoting complex subunit 5 / / APC5 / Cyclosome subunit 5


Mass: 85179.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC5, APC5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX4
#9: Protein Anaphase-promoting complex subunit CDC26 / / Anaphase-promoting complex subunit 12 / APC12 / Cell division cycle protein 26 homolog


Mass: 9793.999 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC26, ANAPC12, C9orf17 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8NHZ8
#10: Protein Anaphase-promoting complex subunit 13 / / APC13 / Cyclosome subunit 13


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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BS18
#11: Protein Anaphase-promoting complex subunit 16 / / APC16 / Cyclosome subunit 16


Mass: 11677.995 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q96DE5
#13: Protein Anaphase-promoting complex subunit 7 / / APC7 / Cyclosome subunit 7


Mass: 66929.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC7, APC7 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX3
#16: Protein Anaphase-promoting complex subunit 11 / / APC11 / Cyclosome subunit 11 / Hepatocellular carcinoma-associated RING finger 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NYG5

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Protein , 2 types, 2 molecules SR

#7: Protein F-box only protein 5 / Early mitotic inhibitor 1


Mass: 50227.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXO5, EMI1, FBX5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKT4
#15: Protein Fizzy-related protein homolog / Fzr / CDC20-like protein 1 / Cdh1/Hct1 homolog / hCDH1


Mass: 55253.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZR1, CDH1, FYR, FZR, KIAA1242 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UM11

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Cell division cycle protein ... , 3 types, 6 molecules KQJPUV

#8: Protein Cell division cycle protein 16 homolog / Cell cycle / Anaphase-promoting complex subunit 6 / APC6 / CDC16 homolog / CDC16Hs / Cyclosome subunit 6


Mass: 71747.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC16, ANAPC6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13042
#12: Protein Cell division cycle protein 27 homolog / Cell cycle / Anaphase-promoting complex subunit 3 / APC3 / CDC27 homolog / CDC27Hs / H-NUC


Mass: 91973.125 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: Trichoplusia ni (cabbage looper) / References: UniProt: P30260
#14: Protein Cell division cycle protein 23 homolog / Cell cycle / Anaphase-promoting complex subunit 8 / APC8 / Cyclosome subunit 8


Mass: 68921.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC23, ANAPC8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX2

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Non-polymers , 1 types, 6 molecules

#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
Type: COMPLEX / Entity ID: #1-#16 / Source: RECOMBINANT
Molecular weightValue: 1.2 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acidHepes1
2200 mMsodium chlorideNaClSodium chloride1
32 mMDithiothreitolDTT1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 8297
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC2.14.2particle selectionTopaz extract with trained models
2EPUimage acquisition
4cryoSPARC2.14.2CTF correctionPatch CTF was used to estimate CTF
7UCSF Chimera1.14model fitting
9PHENIX1.16-3549model refinement
10Coot0.9model refinement
11cryoSPARC2.14.2initial Euler assignment
12cryoSPARC2.14.2final Euler assignment
13RELION3.1 betaclassification
14cryoSPARC2.14.23D reconstructionNon-uniform refinement was used
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1800000 / Details: The particles were automatically selected
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 364331 / Symmetry type: POINT
Atomic model buildingB value: 80 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 4UI9

4ui9

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00572971
ELECTRON MICROSCOPYf_angle_d0.59798762
ELECTRON MICROSCOPYf_dihedral_angle_d2.7248212
ELECTRON MICROSCOPYf_chiral_restr0.04210992
ELECTRON MICROSCOPYf_plane_restr0.00412595

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