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Structural basis for the subunit assembly of the anaphase promoting complex

by single particle reconstruction

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 52, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 52, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1843
TitleStructural basis for the subunit assembly of the anaphase promoting complex
MapApc4 and Apc5
SampleApc4-Apc5 heterodimer
KeywordsAPC/C, anaphase promoting complex
AuthorsSchreiber A, Stengel F, Zhang Z, Enchev RE, Kong E, Morris EP, Robinson CV, daFonseca PCA, Barford D
DateDeposition: 2010-12-04, Header release: 2010-12-09, Map release: 2011-02-07, Last update: 2013-12-11
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 52, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 52, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

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List of similar structure data about Omokage system
Article
Citation - Primary
ArticleNature, Vol. 470, Issue 7333, Page 227-32, Year 2011
TitleStructural basis for the subunit assembly of the anaphase-promoting complex.
AuthorsAnne Schreiber, Florian Stengel, Ziguo Zhang, Radoslav I Enchev, Eric H Kong, Edward P Morris, Carol V Robinson, Paula C A da Fonseca, 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), APC5 protein, S cerevisiae, Amino Acid Motifs, Anaphase-Promoting Complex-Cyclosome (6.3.2.19), Animals, Apc2 Subunit, Anaphase-Promoting Complex-Cyclosome (6.3.2.19), Apc5 Subunit, Anaphase-Promoting Complex-Cyclosome, Apc8 Subunit, Anaphase-Promoting Complex-Cyclosome, Biocatalysis, CDC23 protein, S cerevisiae, Cell Line, Holoenzymes (chemistry), Mass Spectrometry, Microscopy, Electron, Models, Molecular, Molecular Weight, Protein Binding, Protein Conformation, Protein Subunits (chemistry), Recombinant Proteins (chemistry), Saccharomyces cerevisiae (chemistry), Saccharomyces cerevisiae Proteins (chemistry), Scattering, Radiation, Schizosaccharomyces (chemistry), Structure-Activity Relationship, Substrate Specificity, Ubiquitin-Protein Ligase Complexes (chemistry, 6.3.2.19), Ubiquitination
LinksDOI: 10.1038/nature09756, PubMed: 21307936
Map
Fileemd_1843.map.gz ( map file in CCP4 format, 6751 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
120 pix
3.47 A/pix
= 416.4 A
120 pix
3.47 A/pix
= 416.4 A
120 pix
3.47 A/pix
= 416.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:52 (by author), 52 (movie #1):
Minimum - Maximum: -150.097 - 339.789
Average (Standard dev.): 0.606204 (9.63846)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions120120120
Origin-60-60-60
Limit595959
Spacing120120120
Unit CellA= B= C: 416.4 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/z120120120
origin x/y/z0.0000.0000.000
length x/y/z416.400416.400416.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-75-75-74
NX/NY/NZ150150150
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-150.097339.7890.606
Annotation DetailsApc4 and Apc5
Supplement
Images
Images
Sample
NameApc4-Apc5 heterodimer
Number of Components1
Theoretical Mass0.16MDa
Experimental Mass0.155MDa
Component #1: protein - Apc4_5
Scientific nameApc4_5
Scientific Name of SpeciesSaccharomyces cerevisiae

Common Name of SpeciesBaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderEucentric
ModelOTHER
Camera
Processing
Methodsingle particle reconstruction
Single Particle
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1843.xml (5.3 KB)
Map dataemd_1843.map.gz (5.1 MB)
Images1843.gif (77.3 KB)
Apc45_7734_1843.tif (757 KB)
emd_1843.tif (82.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1843
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 27.5 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 27.6 KB