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

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Basic information

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
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: Nat Commun / Year: 2024
Title: Cryo-EM structures of apo-APC/C and APC/C complexes provide insights into APC/C regulation.
Authors: Anna Höfler / Jun Yu / Jing Yang / Ziguo Zhang / Leifu Chang / Stephen H McLaughlin / Geoffrey W Grime / Elspeth F Garman / Andreas Boland / David Barford /
Abstract: APC/C is a multi-subunit complex that functions as a master regulator of cell division. It controls progression through the cell cycle by timely marking mitotic cyclins and other cell cycle ...APC/C is a multi-subunit complex that functions as a master regulator of cell division. It controls progression through the cell cycle by timely marking mitotic cyclins and other cell cycle regulatory proteins for degradation. The APC/C itself is regulated by the sequential action of its coactivator subunits CDC20 and CDH1, post-translational modifications, and its inhibitory binding partners EMI1 and the mitotic checkpoint complex. In this study, we took advantage of developments in cryo-electron microscopy to determine the structures of human APC/C and apo-APC/C at 2.9 Å and 3.2 Å resolution, respectively, providing insights into the regulation of APC/C activity. The high-resolution maps allow the unambiguous assignment of an α-helix to the N-terminus of CDH1 (CDH1) in the APC/C ternary complex. We also identify a zinc-binding module in APC2 that confers structural stability to the complex, and we confirm the presence of zinc ions experimentally. Finally, due to the higher resolution and well defined density of these maps, we are able to build, aided by AlphaFold predictions, several intrinsically disordered regions in different APC/C subunits that likely play a role in proper APC/C assembly and regulation of its activity.
History
DepositionDec 1, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing 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
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 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
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
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
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.2)
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 3.1 beta)

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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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