[English] 日本語
Yorodumi
- PDB-6q6h: Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q6h
TitleCryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D2 box class
Components
  • (Anaphase-promoting complex subunit ...) x 10
  • (Cell division cycle protein ...Cell cycle) x 4
  • Apc1
  • Cyclin-A2
KeywordsCELL CYCLE / spindle assembly checkpoint / anaphase-promoting complex / cyclin / ubiquitination
Function / homology
Function and homology information


Mitotic Prometaphase / Resolution of Sister Chromatid Cohesion / Senescence-Associated Secretory Phenotype (SASP) / DNA Damage/Telomere Stress Induced Senescence / RHO GTPases Activate Formins / Ub-specific processing proteases / Processing of DNA double-strand break ends / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation ...Mitotic Prometaphase / Resolution of Sister Chromatid Cohesion / Senescence-Associated Secretory Phenotype (SASP) / DNA Damage/Telomere Stress Induced Senescence / RHO GTPases Activate Formins / Ub-specific processing proteases / Processing of DNA double-strand break ends / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / G2 Phase / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Cyclin A/B1/B2 associated events during G2/M transition / p53-Dependent G1 DNA Damage Response / Cyclin A:Cdk2-associated events at S phase entry / Antigen processing: Ubiquitination & Proteasome degradation / Separation of Sister Chromatids / APC-Cdc20 mediated degradation of Nek2A / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / Inactivation of APC/C via direct inhibition of the APC/C complex / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / G0 and Early G1 / APC/C:Cdc20 mediated degradation of Cyclin B / Phosphorylation of Emi1 / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / 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 / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Regulation of APC/C activators between G1/S and early anaphase / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of the APC/C / regulation of mitotic cell cycle spindle assembly checkpoint / metaphase/anaphase transition of mitotic cell cycle / regulation of meiotic nuclear division / positive regulation of synapse maturation / ubiquitin-protein transferase activator activity / positive regulation of synaptic plasticity / positive regulation of mitotic metaphase/anaphase transition / anaphase-promoting complex / cullin-RING ubiquitin ligase complex / cellular response to luteinizing hormone stimulus / cellular response to cocaine / anaphase-promoting complex binding / regulation of exit from mitosis / regulation of mitotic metaphase/anaphase transition / cell cycle G1/S phase transition / ubiquitin-ubiquitin ligase activity / positive regulation of ubiquitin protein ligase activity / regulation of dendrite development / mitotic sister chromatid cohesion / mitotic cell cycle phase transition / male pronucleus / protein K11-linked ubiquitination / female pronucleus / cellular response to insulin-like growth factor stimulus / mitotic metaphase plate congression / cellular response to leptin stimulus / response to glucagon / cullin family protein binding / positive regulation of dendrite morphogenesis / cyclin-dependent protein serine/threonine kinase regulator activity / cochlea development / regulation of mitotic cell cycle / cellular response to platelet-derived growth factor stimulus / intracellular / positive regulation of axon extension / condensed chromosome kinetochore / mitotic spindle assembly checkpoint / regulation of DNA replication / mitotic spindle assembly / regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin A2-CDK2 complex / histone phosphorylation / regulation of mitotic cell cycle phase transition / nuclear periphery / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / kinetochore / cellular response to estradiol stimulus / animal organ regeneration / spindle / ubiquitin protein ligase activity / spindle pole / positive regulation of fibroblast proliferation / ubiquitin-protein transferase activity / histone deacetylase binding / cellular response to hypoxia / anaphase-promoting complex-dependent catabolic process / mitotic cell cycle / Ras protein signal transduction / G2/M transition of mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein phosphatase binding / protein C-terminus binding
Tetratricopeptide repeat / Anaphase promoting complex (APC) subunit 2 / Cyclin, N-terminal domain / WD domain, G-beta repeat / Tetratricopeptide repeat / Cullin family / Cyclin, C-terminal domain / Anaphase-promoting complex, subunit 10 (APC10) / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein ...Tetratricopeptide repeat / Anaphase promoting complex (APC) subunit 2 / Cyclin, N-terminal domain / WD domain, G-beta repeat / Tetratricopeptide repeat / Cullin family / Cyclin, C-terminal domain / Anaphase-promoting complex, subunit 10 (APC10) / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein / Anaphase-promoting complex APC subunit CDC26 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 11 RING-H2 finger / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 4 WD40 domain / Anaphase-promoting complex, cyclosome, subunit 4 / Tetratricopeptide repeat / Anaphase-promoting complex subunit 15 / N-terminal region of cyclin_N / Anaphase-promoting complex, subunit 16 / Cyclins signature. / Cyclin / Cyclin-like superfamily / TPR repeat profile. / Anaphase-promoting complex subunit 4 long domain / Anaphase-promoting complex subunit 2, C-terminal / WD40/YVTN repeat-like-containing domain superfamily / Cullin homology domain / Anaphase-promoting complex subunit APC10/Doc1 / Anaphase-promoting complex subunit 4, metazoa / Anaphase-promoting complex, subunit CDC26 / Tetratricopeptide repeat / WD40 repeat, conserved site / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 4, WD40 domain / Winged helix DNA-binding domain superfamily / Anaphase-promoting complex subunit 11 / Anaphase-promoting complex subunit 5 domain / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 16 / Cyclin-A, N-terminal / The WD repeat Cdc20/Fizzy family / Cullin homology domain superfamily / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / Trp-Asp (WD) repeats signature. / Cullin family profile. / Zinc finger, RING/FYVE/PHD-type / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Tetratricopeptide repeat / Trp-Asp (WD) repeats profile. / Zinc finger RING-type profile. / TPR repeat region circular profile. / Trp-Asp (WD) repeats circular profile. / DOC domain profile. / Cyclin-like / WD40-repeat-containing domain / Tetratricopeptide repeat-containing domain / Cyclin, C-terminal domain / Tetratricopeptide-like helical domain superfamily / Tetratricopeptide repeat 1 / WD40 repeat / Zinc finger, RING-type / Cullin, N-terminal / Cyclin, N-terminal / Cdc23 / Apc13 / Galactose-binding-like domain superfamily / APC10/DOC domain
Cell division cycle protein 20 homolog / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / 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 ...Cell division cycle protein 20 homolog / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / 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 / Anaphase-promoting complex subunit 15 / Cell division cycle protein 27 homolog / Cyclin-A2 / Cell division cycle protein 16 homolog
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang, S. / Barford, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1021/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: Cyclin A2 degradation during the spindle assembly checkpoint requires multiple binding modes to the APC/C.
Authors: Suyang Zhang / Thomas Tischer / David Barford /
Abstract: The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are ...The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are both targeted for degradation by the APC/C, during the spindle assembly checkpoint (SAC), the mitotic checkpoint complex (MCC) represses APC/C's activity towards cyclin B1, but not cyclin A2. Through structural, biochemical and in vivo analysis, we identify a non-canonical D box (D2) that is critical for cyclin A2 ubiquitination in vitro and degradation in vivo. During the SAC, cyclin A2 is ubiquitinated by the repressed APC/C-MCC, mediated by the cooperative engagement of its KEN and D2 boxes, ABBA motif, and the cofactor Cks. Once the SAC is satisfied, cyclin A2 binds APC/C-Cdc20 through two mutually exclusive binding modes, resulting in differential ubiquitination efficiency. Our findings reveal that a single substrate can engage an E3 ligase through multiple binding modes, affecting its degradation timing and efficiency.
Validation Report
SummaryFull reportAbout validation report
History
DepositionDec 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4466
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Anaphase-promoting complex subunit 10
D: Anaphase-promoting complex subunit 15
A: Apc1
N: Anaphase-promoting complex subunit 2
I: Anaphase-promoting complex subunit 4
O: Anaphase-promoting complex subunit 5
K: Cell division cycle protein 16 homolog
C: Anaphase-promoting complex subunit 11
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: Cell division cycle protein 20 homolog
S: Cyclin-A2


Theoretical massNumber of molelcules
Total (without water)1,262,16221
Polymers1,262,16221
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area112190 Å2
ΔGint-554 kcal/mol
Surface area333360 Å2
MethodPISA

-
Components

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

#1: Protein/peptide 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: unidentified baculovirus / References: UniProt: Q9UM13
#2: Protein/peptide 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: unidentified baculovirus / References: UniProt: P60006
#4: Protein/peptide 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: unidentified baculovirus / References: UniProt: Q9UJX6
#5: Protein/peptide Anaphase-promoting complex subunit 4 / / APC4 / Cyclosome subunit 4


Mass: 92219.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC4, APC4 / Production host: unidentified baculovirus / References: UniProt: Q9UJX5
#6: Protein/peptide 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: unidentified baculovirus / References: UniProt: Q9UJX4
#8: Protein/peptide 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: unidentified baculovirus / References: UniProt: Q9NYG5
#9: Protein/peptide 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: unidentified baculovirus / References: UniProt: Q8NHZ8
#10: Protein/peptide 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: unidentified baculovirus / References: UniProt: Q9BS18
#11: Protein/peptide 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: unidentified baculovirus / References: UniProt: Q96DE5
#13: Protein/peptide 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: unidentified baculovirus / References: UniProt: Q9UJX3

-
Protein/peptide , 2 types, 2 molecules AS

#3: Protein/peptide Apc1


Mass: 207240.234 Da / Num. of mol.: 1 / Mutation: deletion of residues 307-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus
#16: Protein/peptide Cyclin-A2 / Cyclin-A / Cyclin A


Mass: 44427.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P20248

-
Cell division cycle protein ... , 4 types, 7 molecules KQJPUVR

#7: Protein/peptide 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: unidentified baculovirus / References: UniProt: Q13042
#12: Protein/peptide 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: unidentified baculovirus / References: UniProt: P30260
#14: Protein/peptide 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: unidentified baculovirus / References: UniProt: Q9UJX2
#15: Protein/peptide Cell division cycle protein 20 homolog / Cell cycle / p55CDC


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: unidentified baculovirus / References: UniProt: Q12834

-
Experimental details

-
Experiment

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

-
Sample preparation

Component

Name: Cryo-EM structure of the APC/C-Cdc20-Cdk2-cyclinA2-Cks2 complex, the D2 box class / Type: COMPLEX

IDEntity IDParent-IDSource
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 160MULTIPLE SOURCES
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 151RECOMBINANT
3161RECOMBINANT
Molecular weightValue: 1.3 MDa
Source (natural)

Ncbi tax-ID: 9606 / Organism: Homo sapiens (human)

IDEntity assembly-ID
22
33
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22unidentified baculovirus10469
33Esacherichia coli562
Buffer solutionpH: 8 / Details: 20mM Hepes, 150mM NaCl, 0.5mM TCEP
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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
Image recordingElectron dose: 28 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM softwareName: RELION / Version: 3 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 117044 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more