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- EMDB-1841: Structural basis for the subunit assembly of the anaphase promoti... -

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Basic information

Entry
Database: EMDB / ID: EMD-1841
TitleStructural basis for the subunit assembly of the anaphase promoting complex
Map dataAnaphase promoting complex TPR6 subcomplex
Sample
  • Sample: Anaphase promoting complex TPR6 subcomplex
  • Protein or peptide: Anaphase promoting complex TPR6 subcomplex
  • Protein or peptide: Cdh1
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
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 2, 2010-
Header (metadata) releaseDec 10, 2010-
Map releaseFeb 4, 2011-
UpdateFeb 11, 2011-
Current statusFeb 11, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.075
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.075
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

figure_EBI18...

Downloads & links

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Map

FileDownload / File: emd_1841.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAnaphase promoting complex TPR6 subcomplex
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 SOFTWARE: 0.0133 / Movie #1: 0.075
Minimum - Maximum-0.482671 - 0.771349
Average (Standard dev.)0.00152374 (±0.0274373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-69-70-70
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-70-69-70
NC/NR/NS140140140
D min/max/mean-0.4830.7710.002

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Supplemental data

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Sample components

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Entire : Anaphase promoting complex TPR6 subcomplex

EntireName: Anaphase promoting complex TPR6 subcomplex
Components
  • Sample: Anaphase promoting complex TPR6 subcomplex
  • Protein or peptide: Anaphase promoting complex TPR6 subcomplex
  • Protein or peptide: Cdh1

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Supramolecule #1000: Anaphase promoting complex TPR6 subcomplex

SupramoleculeName: Anaphase promoting complex TPR6 subcomplex / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: Anaphase promoting complex TPR6 subcomplex

MacromoleculeName: Anaphase promoting complex TPR6 subcomplex / type: protein_or_peptide / ID: 1 / Name.synonym: Anaphase promoting complex TPR6 subcomplex / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Bakers' Yeast
Recombinant expressionOrganism: Baculovirus/Insect Cells

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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: Bakers' yeast
Recombinant expressionOrganism: Baculovirus/Insect cells

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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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