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- EMDB-1819: Structure of S. cerevisiae anaphase promoting complex-Cdh1 bound ... -

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Basic information

Entry
Database: EMDB / ID: 1819
TitleStructure of S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
Keywordsanaphase promoting complex / cyclosome / APC / APC/C / cell cycle / D-box / KEN-box / co-activator / Cdh1 / tetraticopeptide repeats / TPR / ubiquitylation / cyclin
SampleS. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
SourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Map dataStructure of S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
Methodsingle particle reconstruction
AuthorsdaFonseca PCA / Kong EH / Zhang Z / Schreiber A / Williams MA / Morris EP / Barford D
CitationNature, 2011, 470, 274-278

Nature, 2011, 470, 274-278 StrPapers
Structures of APC/C(Cdh1) with substrates identify Cdh1 and Apc10 as the D-box co-receptor.
Paula C A da Fonseca / Eric H Kong / Ziguo Zhang / Anne Schreiber / Mark A Williams / Edward P Morris / David Barford

DateDeposition: Oct 27, 2010 / Header (metadata) release: Dec 9, 2010 / Map release: Dec 16, 2010 / Last update: Oct 27, 2010

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.121
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.121
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1819.map.gz (map file in CCP4 format, 10720 KB)
Projections & slices
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AxesY (Sec.)X (Row.)Z (Col.)
140 pix
3.47 A/pix
= 485.8 A
140 pix
3.47 A/pix
= 485.8 A
140 pix
3.47 A/pix
= 485.8 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.47 A
Density
Contour Level:0.121 (by emdb), 0.121 (movie #1):
Minimum - Maximum-0.42908561 - 0.63115054
Average (Standard dev.)0.0017539 (0.02725418)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZXY
Dimensions140140140
Origin-70-70-70
Limit696969
Spacing140140140
CellA=B=C: 485.80002 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-70-70-70
NX/NY/NZ140140140
MAP C/R/S312
start NC/NR/NS-70-70-70
NC/NR/NS140140140
D min/max/mean-0.4290.6310.002

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Supplemental data

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Sample components

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Entire S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment

EntireName: S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
Number of components: 3

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Component #1: protein, Anaphase promoting complex

ProteinName: Anaphase promoting complex / a.k.a: Anaphase promoting complex or cyclosome / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /

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Component #2: protein, Cdh1

ProteinName: Cdh1 / a.k.a: Cdh1 / Recombinant expression: Yes
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Spodoptera frugiperda / arthropod

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Component #3: protein, Hsl1

ProteinName: Hsl1 / a.k.a: Hsl1 fragment / Recombinant expression: Yes
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli

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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

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/A2 / 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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