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- PDB-5khr: Model of human Anaphase-promoting complex/Cyclosome complex (APC1... -

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Entry
Database: PDB / ID: 5khr
TitleModel of human Anaphase-promoting complex/Cyclosome complex (APC15 deletion mutant) in complex with the E2 UBE2C/UBCH10 poised for ubiquitin ligation to substrate (APC/C-CDC20-substrate-UBE2C)
Components
  • (Anaphase-promoting complex subunit ...) x 10
  • (Cell division cycle protein ...Cell cycle) x 4
  • HSL1 peptide
  • Ubiquitin-conjugating enzyme E2 C
KeywordsCELL CYCLE / ubiquitination / protein complex / mitosis
Function / homology
Function and homology information


protein localization to septin ring / mitotic morphogenesis checkpoint signaling / metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / cellular bud neck septin ring / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of exit from mitosis / free ubiquitin chain polymerization ...protein localization to septin ring / mitotic morphogenesis checkpoint signaling / metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / cellular bud neck septin ring / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of exit from mitosis / 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 / 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 / (E3-independent) E2 ubiquitin-conjugating enzyme / regulation of exit from mitosis / positive regulation of synaptic plasticity / Phosphorylation of the APC/C / anaphase-promoting complex binding / 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 / regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / mitotic sister chromatid cohesion / mitotic metaphase chromosome alignment / mitotic spindle assembly checkpoint signaling / ubiquitin conjugating enzyme activity / ubiquitin-like protein ligase binding / regulation of mitotic cell cycle / cullin family protein binding / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / mitotic spindle assembly / protein K48-linked ubiquitination / positive regulation of axon extension / heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / ubiquitin ligase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / 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 / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / brain development / protein catabolic process / 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 / ubiquitin protein ligase activity / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / nervous system development / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / cell differentiation / molecular adaptor activity / protein ubiquitination / regulation of cell cycle / non-specific serine/threonine protein kinase / Ub-specific processing proteases / protein kinase activity / intracellular signal transduction / cell cycle / cell division / phosphorylation / negative regulation of gene expression / protein serine kinase activity / centrosome / protein serine/threonine kinase activity
Similarity search - Function
: / The WD repeat Cdc20/Fizzy family / 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 ...: / The WD repeat Cdc20/Fizzy family / 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 / 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 / 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 / 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
Ubiquitin-conjugating enzyme E2 C / Cell division cycle protein 27 homolog / Probable serine/threonine-protein kinase HSL1 / Cell division cycle protein 20 homolog / 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 ...Ubiquitin-conjugating enzyme E2 C / Cell division cycle protein 27 homolog / Probable serine/threonine-protein kinase HSL1 / Cell division cycle protein 20 homolog / 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 / Anaphase-promoting complex subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsVanderLinden, R. / Yamaguchi, M. / Dube, P. / Haselbach, D. / Stark, H. / Schulman, B.A.
CitationJournal: Mol Cell / Year: 2016
Title: Cryo-EM of Mitotic Checkpoint Complex-Bound APC/C Reveals Reciprocal and Conformational Regulation of Ubiquitin Ligation.
Authors: Masaya Yamaguchi / Ryan VanderLinden / Florian Weissmann / Renping Qiao / Prakash Dube / Nicholas G Brown / David Haselbach / Wei Zhang / Sachdev S Sidhu / Jan-Michael Peters / Holger Stark ...Authors: Masaya Yamaguchi / Ryan VanderLinden / Florian Weissmann / Renping Qiao / Prakash Dube / Nicholas G Brown / David Haselbach / Wei Zhang / Sachdev S Sidhu / Jan-Michael Peters / Holger Stark / Brenda A Schulman /
Abstract: The mitotic checkpoint complex (MCC) coordinates proper chromosome biorientation on the spindle with ubiquitination activities of CDC20-activated anaphase-promoting complex/cyclosome (APC/C(CDC20)). ...The mitotic checkpoint complex (MCC) coordinates proper chromosome biorientation on the spindle with ubiquitination activities of CDC20-activated anaphase-promoting complex/cyclosome (APC/C(CDC20)). APC/C(CDC20) and two E2s, UBE2C and UBE2S, catalyze ubiquitination through distinct architectures for linking ubiquitin (UB) to substrates and elongating polyUB chains, respectively. MCC, which contains a second molecule of CDC20, blocks APC/C(CDC20)-UBE2C-dependent ubiquitination of Securin and Cyclins, while differentially determining or inhibiting CDC20 ubiquitination to regulate spindle surveillance, checkpoint activation, and checkpoint termination. Here electron microscopy reveals conformational variation of APC/C(CDC20)-MCC underlying this multifaceted regulation. MCC binds APC/C-bound CDC20 to inhibit substrate access. However, rotation about the CDC20-MCC assembly and conformational variability of APC/C modulate UBE2C-catalyzed ubiquitination of MCC's CDC20 molecule. Access of UBE2C is limiting for subsequent polyubiquitination by UBE2S. We propose that conformational dynamics of APC/C(CDC20)-MCC modulate E2 activation and determine distinctive ubiquitination activities as part of a response mechanism ensuring accurate sister chromatid segregation.
History
DepositionJun 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / em_image_scans
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Anaphase-promoting complex subunit 1
B: Anaphase-promoting complex subunit 11
C: Cell division cycle protein 23 homolog
E: Anaphase-promoting complex subunit 16
F: Cell division cycle protein 27 homolog
G: Anaphase-promoting complex subunit CDC26
H: Cell division cycle protein 27 homolog
I: Anaphase-promoting complex subunit 4
J: Cell division cycle protein 16 homolog
K: Cell division cycle protein 16 homolog
L: Anaphase-promoting complex subunit 10
M: Anaphase-promoting complex subunit 13
N: Anaphase-promoting complex subunit 2
O: Anaphase-promoting complex subunit 5
P: Cell division cycle protein 23 homolog
Q: Ubiquitin-conjugating enzyme E2 C
R: Cell division cycle protein 20 homolog
S: HSL1 peptide
W: Anaphase-promoting complex subunit CDC26
X: Anaphase-promoting complex subunit 7
Y: Anaphase-promoting complex subunit 7


Theoretical massNumber of molelcules
Total (without water)1,231,15621
Polymers1,231,15621
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Anaphase-promoting complex subunit ... , 10 types, 12 molecules ABEGWILMNOXY

#1: Protein Anaphase-promoting complex subunit 1 / / APC1 / Cyclosome subunit 1 / Mitotic checkpoint regulator / Testis-specific gene 24 protein / Coordinate model: Cα atoms only


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
#2: Protein Anaphase-promoting complex subunit 11 / / APC11 / Cyclosome subunit 11 / Hepatocellular carcinoma-associated RING finger protein / Coordinate model: Cα atoms only


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
#4: Protein Anaphase-promoting complex subunit 16 / / APC16 / Cyclosome subunit 16 / Coordinate model: Cα atoms only


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
#6: Protein Anaphase-promoting complex subunit CDC26 / / Anaphase-promoting complex subunit 12 / APC12 / Cell division cycle protein 26 homolog / Coordinate model: Cα atoms only


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
#7: Protein Anaphase-promoting complex subunit 4 / / APC4 / Cyclosome subunit 4 / Coordinate model: Cα atoms only


Mass: 93207.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Contains the remnant of a C-terminal linker and HRV14 3C protease site.
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC4, APC4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX5
#9: Protein Anaphase-promoting complex subunit 10 / / APC10 / Cyclosome subunit 10 / Coordinate model: Cα atoms only


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
#10: Protein Anaphase-promoting complex subunit 13 / / APC13 / Cyclosome subunit 13 / Coordinate model: Cα atoms only


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 2 / / APC2 / Cyclosome subunit 2 / Coordinate model: Cα atoms only


Mass: 94023.055 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
#12: Protein Anaphase-promoting complex subunit 5 / / APC5 / Cyclosome subunit 5 / Coordinate model: Cα atoms only


Mass: 85249.812 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
#16: Protein Anaphase-promoting complex subunit 7 / / APC7 / Cyclosome subunit 7 / Coordinate model: Cα atoms only


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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX3

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Cell division cycle protein ... , 4 types, 7 molecules CPFHJKR

#3: Protein Cell division cycle protein 23 homolog / Cell cycle / Anaphase-promoting complex subunit 8 / APC8 / Cyclosome subunit 8 / Coordinate model: Cα atoms only


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
#5: Protein Cell division cycle protein 27 homolog / Cell cycle / Anaphase-promoting complex subunit 3 / APC3 / CDC27 homolog / CDC27Hs / H-NUC / Coordinate model: Cα atoms only


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


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
#14: Protein Cell division cycle protein 20 homolog / Cell cycle / p55CDC / Coordinate model: Cα atoms only


Mass: 54796.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC20 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12834

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Protein / Protein/peptide , 2 types, 2 molecules QS

#13: Protein Ubiquitin-conjugating enzyme E2 C / (E3-independent) E2 ubiquitin-conjugating enzyme C / E2 ubiquitin-conjugating enzyme C / UbcH10 / ...(E3-independent) E2 ubiquitin-conjugating enzyme C / E2 ubiquitin-conjugating enzyme C / UbcH10 / Ubiquitin carrier protein C / Ubiquitin-protein ligase C / Coordinate model: Cα atoms only


Mass: 20748.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Contains the remnant of a C-terminal linker and HRV14 3C protease site.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2C, UBCH10 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: O00762, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#15: Protein/peptide HSL1 peptide / Coordinate model: Cα atoms only


Mass: 3783.135 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Contains azidohomoalanine in place of K788 and is cross-linked to UBE2C and UB.
Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34244*PLUS

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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: Multi-protein complex of APC/C with coactivator CDC20 and cross-linked UBE2C-UB-Substrate complex mimicking ubiquitination
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 222697 / Symmetry type: POINT

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