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- EMDB-1845: Structural basis for the subunit assembly of the anaphase promoti... -

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Basic information

Entry
Database: EMDB / ID: EMD-1845
TitleStructural basis for the subunit assembly of the anaphase promoting complex
Map dataSC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23)
Sample
  • Sample: SC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23)
  • Protein or peptide: Apc1
  • Protein or peptide: Apc2
  • Protein or peptide: Apc4
  • Protein or peptide: Apc5
  • Protein or peptide: Apc10
  • Protein or peptide: Apc11
  • Protein or peptide: Mnd2
  • Protein or peptide: Cdc23
KeywordsAPC/C / anaphase promoting complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction
AuthorsSchreiber A / Stengel F / Zhang Z / Enchev RE / Kong E / Morris EP / Robinson CV / daFonseca PCA / Barford D
CitationJournal: Nature / Year: 2011
Title: Structural basis for the subunit assembly of the anaphase-promoting complex.
Authors: Anne Schreiber / Florian Stengel / Ziguo Zhang / Radoslav I Enchev / Eric H Kong / Edward P Morris / Carol V Robinson / Paula C A da Fonseca / David Barford /
Abstract: The anaphase-promoting complex or cyclosome (APC/C) is an unusually large E3 ubiquitin ligase responsible for regulating defined cell cycle transitions. Information on how its 13 constituent proteins ...The anaphase-promoting complex or cyclosome (APC/C) is an unusually large E3 ubiquitin ligase responsible for regulating defined cell cycle transitions. Information on how its 13 constituent proteins are assembled, and how they interact with co-activators, substrates and regulatory proteins is limited. Here, we describe a recombinant expression system that allows the reconstitution of holo APC/C and its sub-complexes that, when combined with electron microscopy, mass spectrometry and docking of crystallographic and homology-derived coordinates, provides a precise definition of the organization and structure of all essential APC/C subunits, resulting in a pseudo-atomic model for 70% of the APC/C. A lattice-like appearance of the APC/C is generated by multiple repeat motifs of most APC/C subunits. Three conserved tetratricopeptide repeat (TPR) subunits (Cdc16, Cdc23 and Cdc27) share related superhelical homo-dimeric architectures that assemble to generate a quasi-symmetrical structure. Our structure explains how this TPR sub-complex, together with additional scaffolding subunits (Apc1, Apc4 and Apc5), coordinate the juxtaposition of the catalytic and substrate recognition module (Apc2, Apc11 and Apc10 (also known as Doc1)), and TPR-phosphorylation sites, relative to co-activator, regulatory proteins and substrates.
History
DepositionDec 4, 2010-
Header (metadata) releaseDec 10, 2010-
Map releaseFeb 4, 2011-
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: 47
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 47
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1845.tif

Downloads & links

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Map

FileDownload / File: emd_1845.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (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 AUTHOR: 47.0 / Movie #1: 47
Minimum - Maximum-157.741000000000014 - 222.306000000000012
Average (Standard dev.)0.82479 (±9.57382)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-70-70-70
Dimensions140140140
Spacing140140140
CellA=B=C: 485.8 Å
α=β=γ: 90 °

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-30-24-70
NX/NY/NZ6149141
MAP C/R/S123
start NC/NR/NS-70-70-70
NC/NR/NS140140140
D min/max/mean-157.741222.3060.825

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Supplemental data

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Sample components

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Entire : SC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23)

EntireName: SC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23)
Components
  • Sample: SC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23)
  • Protein or peptide: Apc1
  • Protein or peptide: Apc2
  • Protein or peptide: Apc4
  • Protein or peptide: Apc5
  • Protein or peptide: Apc10
  • Protein or peptide: Apc11
  • Protein or peptide: Mnd2
  • Protein or peptide: Cdc23

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Supramolecule #1000: SC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23)

SupramoleculeName: SC8 (consisting of Apc1, Apc2, Apc4, Apc5, Apc10, Apc11, Mnd2, Cdc23)
type: sample / ID: 1000 / Number unique components: 8
Molecular weightExperimental: 700 KDa / Theoretical: 690 KDa

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Macromolecule #1: Apc1

MacromoleculeName: Apc1 / type: protein_or_peptide / ID: 1 / Name.synonym: Apc1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

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Macromolecule #2: Apc2

MacromoleculeName: Apc2 / type: protein_or_peptide / ID: 2 / Name.synonym: Apc2 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

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Macromolecule #3: Apc4

MacromoleculeName: Apc4 / type: protein_or_peptide / ID: 3 / Name.synonym: Apc4 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

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Macromolecule #4: Apc5

MacromoleculeName: Apc5 / type: protein_or_peptide / ID: 4 / Name.synonym: Apc5 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

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Macromolecule #5: Apc10

MacromoleculeName: Apc10 / type: protein_or_peptide / ID: 5 / Name.synonym: Apc10 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

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Macromolecule #6: Apc11

MacromoleculeName: Apc11 / type: protein_or_peptide / ID: 6 / Name.synonym: Apc11 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

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Macromolecule #7: Mnd2

MacromoleculeName: Mnd2 / type: protein_or_peptide / ID: 7 / Name.synonym: Mnd2 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

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Macromolecule #8: Cdc23

MacromoleculeName: Cdc23 / type: protein_or_peptide / ID: 8 / Name.synonym: Cdc23 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / 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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