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- EMDB-13932: Focused refined map of the catalytic module of the Anaphase-promo... -

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Entry
Database: EMDB / ID: EMD-13932
TitleFocused refined map of the catalytic module of the Anaphase-promoting complex/cyclosome (APC/C).
Map dataFocused refined map (sharpened with deepEMhancer) of the catalytic module of the Anaphase-promoting complex/cyclosome (APC/C).
Sample
  • Complex: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
KeywordsAPC/C / cyclosome / Cdc20 / Cdh1 / ubiquitination / Emi1 / mitosis / Cell cycle
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 / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / vesicle organization / Phosphorylation of Emi1 / anaphase-promoting complex / lens fiber cell differentiation / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / 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 ligase inhibitor activity / ubiquitin-ubiquitin ligase 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 / mitotic G2 DNA damage checkpoint signaling / cullin family protein binding / negative regulation of cellular senescence / 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 / regulation of mitotic cell cycle / 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 / mitotic spindle / kinetochore / spindle / CDK-mediated phosphorylation and removal of Cdc6 / ubiquitin-protein transferase activity / Separation of Sister Chromatids / microtubule cytoskeleton / ubiquitin protein ligase activity / 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 8 / Cdc23 / Apc13p protein / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 4 long domain / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 5 domain / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex, cyclosome, subunit 4 / 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 / F-box domain / Tetratricopeptide repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Cullin / Tetratricopeptide repeat / 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 / 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsHoefler A / Yu J / Chang L / Zhang Z / Yang J / Boland A / Barford D
Funding support Switzerland, United Kingdom, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_185235 Switzerland
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, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13932.png

Downloads & links

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Map

FileDownload / File: emd_13932.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refined map (sharpened with deepEMhancer) of the catalytic module of the Anaphase-promoting complex/cyclosome (APC/C).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.044571437 - 2.1270947
Average (Standard dev.)0.0011316669 (±0.023876008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z385.200385.200385.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0452.1270.001

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Supplemental data

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Additional map: Focused refined map (unsharpened) of the catalytic module...

Fileemd_13932_additional_1.map
AnnotationFocused refined map (unsharpened) of the catalytic module of the Anaphase-promoting complex/cyclosome (APC/C).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the catalytic module of...

Fileemd_13932_half_map_1.map
AnnotationHalf map A of the catalytic module of the Anaphase-promoting complex/cyclosome (APC/C).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the catalytic module of...

Fileemd_13932_half_map_2.map
AnnotationHalf map B of the catalytic module of the Anaphase-promoting complex/cyclosome (APC/C).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Anaphase-promoting complex (APC/C) bound to co-activator Cdh1

EntireName: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
Components
  • Complex: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1

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Supramolecule #1: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1

SupramoleculeName: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.2 MDa

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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
Component:
ConcentrationFormulaName
20.0 mMHepes2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
200.0 mMNaClSodium chloridesodium chloride
2.0 mMDTTDithiothreitol
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 8297 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1800000 / Details: The particles were automatically selected
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.2)
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 3.1 beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14.2) / Software - details: Local Refinement / Number images used: 148755

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Atomic model buiding 1

Initial modelPDB ID:

4ui9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 80

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