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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: 1841
TitleStructural basis for the subunit assembly of the anaphase promoting complex
Keywordsanaphase promoting complex / cyclosome / APC / APC/C / cell cycle / D-box / KEN-box / co-activator / Cdh1 / tetraticopeptide repeats / TPR / ubiquitylation / cyclin
SampleAnaphase promoting complex TPR6 subcomplex
SourceSaccharomyces cerevisiae / yeast / Bakers' Yeast, Bakers' yeast / サッカロミセス・セレビシエ /
Map dataAnaphase promoting complex TPR6 subcomplex
Methodsingle particle reconstruction
AuthorsSchreiber A / Stengel F / Zhang Z / Enchev RE / Kong E / Morris EP / Robinson CV / daFonseca PCA / Barford D
CitationNature, 2011, 470, 227-232

Nature, 2011, 470, 227-232 Yorodumi Papers
Structural basis for the subunit assembly of the anaphase-promoting complex.
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

DateDeposition: Dec 2, 2010 / Header (metadata) release: Dec 10, 2010 / Map release: Feb 4, 2011 / Last update: Feb 11, 2011

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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
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1841.map.gz (map file in CCP4 format, 10720 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
140 pix
3.47 Å/pix.
= 485.8 Å
140 pix
3.47 Å/pix.
= 485.8 Å
140 pix
3.47 Å/pix.
= 485.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.47 Å
Density
Contour Level:0.0133 (by software), 0.075 (movie #1):
Minimum - Maximum-0.482671 - 0.771349
Average (Standard dev.)0.00152374 (0.0274373)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions140140140
Origin-69-70-70
Limit706969
Spacing140140140
CellA=B=C: 485.8 Å
α=β=γ: 90 deg.

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 / Number of components: 1

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Component #1: protein, Anaphase promoting complex TPR6 subcomplex

ProteinName: Anaphase promoting complex TPR6 subcomplex / a.k.a: Anaphase promoting complex TPR6 subcomplex / Recombinant expression: Yes
SourceSpecies: Saccharomyces cerevisiae / yeast / Bakers' Yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Baculovirus/Insect Cells / virus

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Component #2: protein, Cdh1

ProteinName: Cdh1 / a.k.a: Cdh1 / Recombinant expression: Yes
SourceSpecies: Saccharomyces cerevisiae / yeast / Bakers' yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Baculovirus/Insect cells / virus

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Experimental details

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Sample preparation

Specimen stateparticle
StainingGrids were stained using 2% w/v uranyl acetate
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Details: Sample stained using uranyl acetate and imaged at room temperature
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 100 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Room temperature side entry / Model: OTHER
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)

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