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- EMDB-1140: Localization of the coactivator Cdh1 and the cullin subunit Apc2 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1140
TitleLocalization of the coactivator Cdh1 and the cullin subunit Apc2 in a cryo-electron microscopy model of vertebrate APC/C.
Map dataThis is the 3D map of the Xenopus anaphase promoting complex (APC/C)
Sample
  • Sample: Anaphase Promoting Complex
  • Protein or peptide: Anaphase Promoting Complex
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 24.0 Å
AuthorsDube P / Herzog F / Peters JM / Stark H
CitationJournal: Mol Cell / Year: 2005
Title: Localization of the coactivator Cdh1 and the cullin subunit Apc2 in a cryo-electron microscopy model of vertebrate APC/C.
Authors: Prakash Dube / Franz Herzog / Christian Gieffers / Bjoern Sander / Dietmar Riedel / Shirley A Müller / Andreas Engel / Jan-Michael Peters / Holger Stark /
Abstract: The anaphase-promoting complex/cyclosome (APC/C) is a ubiquitin ligase with essential functions in mitosis, meiosis, and G1 phase of the cell cycle. APC/C recognizes substrates via coactivator ...The anaphase-promoting complex/cyclosome (APC/C) is a ubiquitin ligase with essential functions in mitosis, meiosis, and G1 phase of the cell cycle. APC/C recognizes substrates via coactivator proteins such as Cdh1, and bound substrates are ubiquitinated by E2 enzymes that interact with a hetero-dimer of the RING subunit Apc11 and the cullin Apc2. We have obtained three-dimensional (3D) models of human and Xenopus APC/C by angular reconstitution and random conical tilt (RCT) analyses of negatively stained cryo-electron microscopy (cryo-EM) preparations, have determined the masses of these particles by scanning transmission electron microscopy (STEM), and have mapped the locations of Cdh1 and Apc2. These proteins are located on the same side of the asymmetric APC/C, implying that this is where substrates are ubiquitinated. We have further identified a large flexible domain in APC/C that adopts a different orientation upon Cdh1 binding. Cdh1 may thus activate APC/C both by recruiting substrates and by inducing conformational changes.
History
DepositionJul 28, 2005-
Header (metadata) releaseJul 28, 2005-
Map releaseJul 28, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1140.gif

Downloads & links

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Map

FileDownload / File: emd_1140.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the 3D map of the Xenopus anaphase promoting complex (APC/C)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.32 Å/pix.
x 160 pix.
= 530.88 Å		3.32 Å/pix.
x 160 pix.
= 530.88 Å		3.32 Å/pix.
x 160 pix.
= 530.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.318 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.169 / Movie #1: 0.12
Minimum - Maximum-0.39647 - 0.616425
Average (Standard dev.)-0.000174566 (±0.0515504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 530.88 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.3183.3183.318
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z530.880530.880530.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-0.3960.616-0.000

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Supplemental data

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Sample components

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Entire : Anaphase Promoting Complex

EntireName: Anaphase Promoting Complex
Components
  • Sample: Anaphase Promoting Complex
  • Protein or peptide: Anaphase Promoting Complex

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Supramolecule #1000: Anaphase Promoting Complex

SupramoleculeName: Anaphase Promoting Complex / type: sample / ID: 1000 / Oligomeric state: Monomer / Number unique components: 1
Molecular weightExperimental: 1.5 MDa / Method: STEM

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Macromolecule #1: Anaphase Promoting Complex

MacromoleculeName: Anaphase Promoting Complex / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Xenopus laevis (African clawed frog) / synonym: Xenopus

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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

BufferpH: 7.6 / Details: 20 mM Hepes, 150 mM NaCl, 0.5 mM DTT
StainingType: NEGATIVE / Details: carbon sandwich in 2% w/v uranyl formate
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 90500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal magnification: 90500
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: OTHER / Software - Name: Imagic-5

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