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- EMDB-1815: The structure of anaphase promoting complex-Cdh1-Dbox at 10 Angst... -

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Basic information

Entry
Database: EMDB / ID: EMD-1815
TitleThe structure of anaphase promoting complex-Cdh1-Dbox at 10 Angstroms resolution
Map dataThe anaphase promoting complex-Cdh1-Dbox at 10 Angstroms resolution
Sample
  • Sample: S. cerevisiae anaphase promoting complex bound to Cdh1 and a D-box peptide
  • Protein or peptide: Anaphase promoting complex
Keywordsanaphase promoting complex / cyclosome / APC / APC/C / cell cycle / D-box / KEN-box / co-activator / Cdh1 / tetraticopeptide repeats / TPR / ubiquitylation / cyclin
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsdaFonseca PCA / Kong EH / Zhang Z / Schreiber A / Williams MA / Morris EP / Barford D
CitationJournal: Nature / Year: 2011
Title: Structures of APC/C(Cdh1) with substrates identify Cdh1 and Apc10 as the D-box co-receptor.
Authors: Paula C A da Fonseca / Eric H Kong / Ziguo Zhang / Anne Schreiber / Mark A Williams / Edward P Morris / David Barford /
Abstract: The ubiquitylation of cell-cycle regulatory proteins by the large multimeric anaphase-promoting complex (APC/C) controls sister chromatid segregation and the exit from mitosis. Selection of APC/C ...The ubiquitylation of cell-cycle regulatory proteins by the large multimeric anaphase-promoting complex (APC/C) controls sister chromatid segregation and the exit from mitosis. Selection of APC/C targets is achieved through recognition of destruction motifs, predominantly the destruction (D)-box and KEN (Lys-Glu-Asn)-box. Although this process is known to involve a co-activator protein (either Cdc20 or Cdh1) together with core APC/C subunits, the structural basis for substrate recognition and ubiquitylation is not understood. Here we investigate budding yeast APC/C using single-particle electron microscopy and determine a cryo-electron microscopy map of APC/C in complex with the Cdh1 co-activator protein (APC/C(Cdh1)) bound to a D-box peptide at ∼10 Å resolution. We find that a combined catalytic and substrate-recognition module is located within the central cavity of the APC/C assembled from Cdh1, Apc10--a core APC/C subunit previously implicated in substrate recognition--and the cullin domain of Apc2. Cdh1 and Apc10, identified from difference maps, create a co-receptor for the D-box following repositioning of Cdh1 towards Apc10. Using NMR spectroscopy we demonstrate specific D-box-Apc10 interactions, consistent with a role for Apc10 in directly contributing towards D-box recognition by the APC/C(Cdh1) complex. Our results rationalize the contribution of both co-activator and core APC/C subunits to D-box recognition and provide a structural framework for understanding mechanisms of substrate recognition and catalysis by the APC/C.
History
DepositionOct 26, 2010-
Header (metadata) releaseDec 9, 2010-
Map releaseDec 17, 2010-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

figure_EMD18...

Downloads & links

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Map

FileDownload / File: emd_1815.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe anaphase promoting complex-Cdh1-Dbox at 10 Angstroms resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.82 Å/pix.
x 180 pix.
= 508.32 Å		2.82 Å/pix.
x 180 pix.
= 508.32 Å		2.82 Å/pix.
x 180 pix.
= 508.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-11.4368 - 25.5943
Average (Standard dev.)-0.00000000846226 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-89-90-90
Dimensions180180180
Spacing180180180
CellA=B=C: 508.32 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.8242.8242.824
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z508.320508.320508.320
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-90-89-90
NC/NR/NS180180180
D min/max/mean-11.43725.594-0.000

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Supplemental data

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Sample components

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Entire : S. cerevisiae anaphase promoting complex bound to Cdh1 and a D-bo...

EntireName: S. cerevisiae anaphase promoting complex bound to Cdh1 and a D-box peptide
Components
  • Sample: S. cerevisiae anaphase promoting complex bound to Cdh1 and a D-box peptide
  • Protein or peptide: Anaphase promoting complex

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Supramolecule #1000: S. cerevisiae anaphase promoting complex bound to Cdh1 and a D-bo...

SupramoleculeName: S. cerevisiae anaphase promoting complex bound to Cdh1 and a D-box peptide
type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 1.13 MDa

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Macromolecule #1: Anaphase promoting complex

MacromoleculeName: Anaphase promoting complex / type: protein_or_peptide / ID: 1 / Name.synonym: Anaphase promoting complex or cyclosome / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

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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

VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot / Method: Blot for 5 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 95 K
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 62000
Sample stageSpecimen holder: Side entry / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.5 CUT-OFF

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