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- EMDB-1819: Structure of S. cerevisiae anaphase promoting complex-Cdh1 bound ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1819
TitleStructure of S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
Map dataStructure of S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
Sample
  • Sample: S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
  • Protein or peptide: Anaphase promoting complex
  • Protein or peptide: Cdh1
  • Protein or peptide: Hsl1
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 / negative staining
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 27, 2010-
Header (metadata) releaseDec 9, 2010-
Map releaseDec 16, 2010-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.121
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.121
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

figure_EMD18...

Downloads & links

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Map

FileDownload / File: emd_1819.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
3.47 Å/pix.
x 140 pix.
= 485.8 Å		3.47 Å/pix.
x 140 pix.
= 485.8 Å		3.47 Å/pix.
x 140 pix.
= 485.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.47 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.121 / Movie #1: 0.121
Minimum - Maximum-0.42908561 - 0.63115054
Average (Standard dev.)0.0017539 (±0.02725418)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-70-70-70
Dimensions140140140
Spacing140140140
CellA=B=C: 485.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.473.473.47
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z485.800485.800485.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-70-70-70
NX/NY/NZ140140140
MAP C/R/S312
start NC/NR/NS-70-70-70
NC/NR/NS140140140
D min/max/mean-0.4290.6310.002

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Supplemental data

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Sample components

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Entire : S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment

EntireName: S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
Components
  • Sample: S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
  • Protein or peptide: Anaphase promoting complex
  • Protein or peptide: Cdh1
  • Protein or peptide: Hsl1

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Supramolecule #1000: S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment

SupramoleculeName: S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
type: sample / ID: 1000 / Number unique components: 3

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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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Macromolecule #2: Cdh1

MacromoleculeName: Cdh1 / type: protein_or_peptide / ID: 2 / Name.synonym: Cdh1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #3: Hsl1

MacromoleculeName: Hsl1 / type: protein_or_peptide / ID: 3 / Name.synonym: Hsl1 fragment / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

StainingType: NEGATIVE / Details: Grids were stained using 2% w/v uranyl acetate
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
DetailsSample stained using uranyl acetate and imaged at room temperature
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 100 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder: Room temperature side entry / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric)

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