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

by single particle reconstruction

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.121, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.121, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1819
TitleStructure of S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
MapStructure of S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
SampleS. 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
AuthorsdaFonseca PCA, Kong EH, Zhang Z, Schreiber A, Williams MA, Morris EP, Barford D
DateDeposition: 2010-10-27, Header release: 2010-12-09, Map release: 2010-12-16, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.121, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.121, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
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Cite: data citing same article

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Article
Citation - Primary
ArticleNature, Vol. 470, Issue 7333, Page 274-8, Year 2011
TitleStructures of APC/C(Cdh1) with substrates identify Cdh1 and Apc10 as the D-box co-receptor.
AuthorsPaula C A da Fonseca, Eric H Kong, Ziguo Zhang, Anne Schreiber, Mark A Williams, Edward P Morris, David Barford
Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK.
KeywordsAPC2 protein, S cerevisiae (6.3.2.19), Amino Acid Motifs, Anaphase-Promoting Complex-Cyclosome (6.3.2.19), Apc10 Subunit, Anaphase-Promoting Complex-Cyclosome, Apc2 Subunit, Anaphase-Promoting Complex-Cyclosome (6.3.2.19), Biocatalysis, CDH1 protein, S cerevisiae, Cdh1 Proteins, Cell Cycle Proteins (chemistry), Cryoelectron Microscopy, DOC1 protein, S cerevisiae, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Peptides (chemistry), Protein Binding, Protein Conformation, Saccharomyces cerevisiae (chemistry), Saccharomyces cerevisiae Proteins (chemistry), Substrate Specificity, Ubiquitin-Protein Ligase Complexes (chemistry, 6.3.2.19), Ubiquitination
LinksDOI: 10.1038/nature09625, PubMed: 21107322, PMC: PMC3037847
Map
Fileemd_1819.map.gz ( map file in CCP4 format, 10720 KB )
Projections & SlicesSize of images:
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.

Density
Contour Level:0.121 (by emdb), 0.121 (movie #1):
Minimum - Maximum: -0.42908561 - 0.63115054
Average (Standard dev.): 0.0017539 (0.02725418)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderZXY
Dimensions140140140
Origin-70-70-70
Limit696969
Spacing140140140
Unit CellA= B= C: 485.80002 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.47 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.4290.6310.002
Annotation DetailsStructure of S. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
Supplement
Images
Images
Sample
NameS. cerevisiae anaphase promoting complex-Cdh1 bound to a Hsl1 fragment
Number of Components3
Component #1: protein - Anaphase promoting complex or cyclosome
Scientific nameAnaphase promoting complex
Common NameAnaphase promoting complex or cyclosome
Scientific Name of SpeciesSaccharomyces cerevisiae

Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
Recombinant expressionNo
Component #2: protein - Cdh1
Scientific nameCdh1
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 7108
Expression system: Spodoptera frugiperda
Component #3: protein - Hsl1 fragment
Scientific nameHsl1
Common NameHsl1 fragment
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 469008
Expression system: Escherichia coli BL21(DE3)
Experiment
Sample Preparation
StainingGrids were stained using 2% w/v uranyl acetate
Specimen Stateparticle
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI F20
DetailsSample stained using uranyl acetate and imaged at room temperature
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose100 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderRoom temperature side entry
ModelOTHER
Camera
DetectorTVIPS TEMCAM-F415 (4k x 4k)
Processing
Methodsingle particle reconstruction
Single Particle
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1819.xml (7.2 KB)
Map dataemd_1819.map.gz (10 MB)
Imagesfigure_EMD1819.tif (208.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1819
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.4 KB