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- EMDB-1822: Yeast Anaphase Promoting Complex (Dimer) -

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Basic information

Entry
Database: EMDB / ID: EMD-1822
TitleYeast Anaphase Promoting Complex (Dimer)
Map data3D structure of the Yeast Anaphase Promoting Complex (Dimer)
Sample
  • Sample: Yeast anaphase promoting complex (Dimer)
  • Organelle or cellular component: APCC
KeywordsAnaphase / Yeast / Cell cycle
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 35.0 Å
AuthorsBuschhorn BA / Petzold G / Galova M / Dube P / Kraft C / Herzog F / Peters JM / Stark H
CitationJournal: Nat Struct Mol Biol / Year: 2011
Title: Substrate binding on the APC/C occurs between the coactivator Cdh1 and the processivity factor Doc1.
Authors: Bettina A Buschhorn / Georg Petzold / Marta Galova / Prakash Dube / Claudine Kraft / Franz Herzog / Holger Stark / Jan-Michael Peters /
Abstract: The anaphase-promoting complex/cyclosome (APC/C) is a 22S ubiquitin ligase complex that initiates chromosome segregation and mitotic exit. We have used biochemical and electron microscopic analyses ...The anaphase-promoting complex/cyclosome (APC/C) is a 22S ubiquitin ligase complex that initiates chromosome segregation and mitotic exit. We have used biochemical and electron microscopic analyses of Saccharomyces cerevisiae and human APC/C to address how the APC/C subunit Doc1 contributes to recruitment and processive ubiquitylation of APC/C substrates, and to understand how APC/C monomers interact to form a 36S dimeric form. We show that Doc1 interacts with Cdc27, Cdc16 and Apc1 and is located in the vicinity of the cullin-RING module Apc2-Apc11 in the inner cavity of the APC/C. Substrate proteins also bind in the inner cavity, in close proximity to Doc1 and the coactivator Cdh1, and induce conformational changes in Apc2-Apc11. Our results suggest that substrates are recruited to the APC/C by binding to a bipartite substrate receptor composed of a coactivator protein and Doc1.
History
DepositionNov 15, 2010-
Header (metadata) releaseMar 16, 2012-
Map releaseMar 16, 2012-
UpdateMar 16, 2012-
Current statusMar 16, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1822.png

Downloads & links

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Map

FileDownload / File: emd_1822.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D structure of the Yeast Anaphase Promoting Complex (Dimer)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.2 Å/pix.
x 64 pix.
= 460.8 Å		7.2 Å/pix.
x 64 pix.
= 460.8 Å		7.2 Å/pix.
x 64 pix.
= 460.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.30840886 - 0.58570647
Average (Standard dev.)-0.00016378 (±0.05598781)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 460.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.27.27.2
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z460.800460.800460.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-70-70-70
NX/NY/NZ140140140
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.3080.586-0.000

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Supplemental data

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Sample components

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Entire : Yeast anaphase promoting complex (Dimer)

EntireName: Yeast anaphase promoting complex (Dimer)
Components
  • Sample: Yeast anaphase promoting complex (Dimer)
  • Organelle or cellular component: APCC

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Supramolecule #1000: Yeast anaphase promoting complex (Dimer)

SupramoleculeName: Yeast anaphase promoting complex (Dimer) / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: APCC

SupramoleculeName: APCC / type: organelle_or_cellular_component / ID: 1 / Name.synonym: APCC / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Bakers' yeast

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

StainingType: NEGATIVE / Details: Staining with 1% uranyl formate
VitrificationCryogen name: NITROGEN / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Image recordingDigitization - Sampling interval: 1.8 µm
Electron beamAcceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 1271

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