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- EMDB-2653: Cryo-EM structure of human APC/C (Apc11-RING deletion) at 8.0 A r... -

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Basic information

Entry
Database: EMDB / ID: EMD-2653
TitleCryo-EM structure of human APC/C (Apc11-RING deletion) at 8.0 A resolution
Map dataReconstruction of recombinant APC/C (Apc11-RING deletion)
Sample
  • Sample: Reconstruction of recombinant APC/C (Apc11-RING deletion)
  • Protein or peptide: Anaphase-promoting complex
KeywordsCullin-RING E3 ligase / Ubiquitination
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsChang LF / Zhang Z / Yang J / McLaughlin S / Barford D
CitationJournal: Nature / Year: 2014
Title: Molecular architecture and mechanism of the anaphase-promoting complex.
Authors: Lei-Fu Chang / Ziguo Zhang / Jing Yang / Stephen H McLaughlin / David Barford /
Abstract: The ubiquitination of cell cycle regulatory proteins by the anaphase-promoting complex/cyclosome (APC/C) controls sister chromatid segregation, cytokinesis and the establishment of the G1 phase of ...The ubiquitination of cell cycle regulatory proteins by the anaphase-promoting complex/cyclosome (APC/C) controls sister chromatid segregation, cytokinesis and the establishment of the G1 phase of the cell cycle. The APC/C is an unusually large multimeric cullin-RING ligase. Its activity is strictly dependent on regulatory coactivator subunits that promote APC/C-substrate interactions and stimulate its catalytic reaction. Because the structures of many APC/C subunits and their organization within the assembly are unknown, the molecular basis for these processes is poorly understood. Here, from a cryo-electron microscopy reconstruction of a human APC/C-coactivator-substrate complex at 7.4 Å resolution, we have determined the complete secondary structural architecture of the complex. With this information we identified protein folds for structurally uncharacterized subunits, and the definitive location of all 20 APC/C subunits within the 1.2 MDa assembly. Comparison with apo APC/C shows that the coactivator promotes a profound allosteric transition involving displacement of the cullin-RING catalytic subunits relative to the degron-recognition module of coactivator and APC10. This transition is accompanied by increased flexibility of the cullin-RING subunits and enhanced affinity for UBCH10-ubiquitin, changes which may contribute to coactivator-mediated stimulation of APC/C E3 ligase activity.
History
DepositionMay 17, 2014-
Header (metadata) releaseJun 18, 2014-
Map releaseJul 30, 2014-
UpdateSep 17, 2014-
Current statusSep 17, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2653.jpg

Downloads & links

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Map

FileDownload / File: emd_2653.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of recombinant APC/C (Apc11-RING deletion)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.36 Å/pix.
x 160 pix.
= 377.6 Å		2.36 Å/pix.
x 160 pix.
= 377.6 Å		2.36 Å/pix.
x 160 pix.
= 377.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.06 / Movie #1: 0.05
Minimum - Maximum-0.10351484 - 0.24579199
Average (Standard dev.)0.00044269 (±0.01227892)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 377.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.362.362.36
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z377.600377.600377.600
α/β/γ90.00090.00090.000
start NX/NY/NZ0-51-100
NX/NY/NZ82103201
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-0.1040.2460.000

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Supplemental data

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Sample components

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Entire : Reconstruction of recombinant APC/C (Apc11-RING deletion)

EntireName: Reconstruction of recombinant APC/C (Apc11-RING deletion)
Components
  • Sample: Reconstruction of recombinant APC/C (Apc11-RING deletion)
  • Protein or peptide: Anaphase-promoting complex

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Supramolecule #1000: Reconstruction of recombinant APC/C (Apc11-RING deletion)

SupramoleculeName: Reconstruction of recombinant APC/C (Apc11-RING deletion)
type: sample / ID: 1000 / Number unique components: 14
Molecular weightExperimental: 1.2 MDa / Theoretical: 1.2 MDa

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Macromolecule #1: Anaphase-promoting complex

MacromoleculeName: Anaphase-promoting complex / type: protein_or_peptide / ID: 1 / Name.synonym: Cyclosome / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TECNAI F20
DateApr 1, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder: Gatan 626 cryo-holder / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 143783

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