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Localization of the coactivator Cdh1 and the cullin subunit Apc2 in a cryo-electron microscopy model of vertebrate APC/C.
by single particle reconstruction, at 24 A resolution
#1: Surface view with section colored by density value, Surface level: 0.106, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 0.106, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1142 |
|---|---|
| Title | Localization of the coactivator Cdh1 and the cullin subunit Apc2 in a cryo-electron microscopy model of vertebrate APC/C. |
| Map | This is a 3D map of the Xenopus APC/C in complex with an activator Cdh1 |
| Sample | Anaphase Promoting Complex |
| Authors | Dube P, Herzog F, Peters JM, Stark H |
| Date | Deposition: 2005-07-28, Header release: 2005-07-28, Map release: 2006-07-28, Last update: 2011-08-05 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 0.106, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.106, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Mol. Cell, Vol. 20, Issue 6, Page 867-79, Year 2005 |
|---|---|
| Title | Localization of the coactivator Cdh1 and the cullin subunit Apc2 in a cryo-electron microscopy model of vertebrate APC/C. |
| Authors | Prakash Dube, Franz Herzog, Christian Gieffers, Bjoern Sander, Dietmar Riedel, Shirley A Müller, Andreas Engel, Jan-Michael Peters, Holger Stark Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany. |
| Keywords |  Animals, Cryoelectron Microscopy, Cullin Proteins (analysis), HeLa Cells, Humans, Models, Molecular, Molecular Weight, Protein Conformation, Protein Subunits (chemistry), Ubiquitin (metabolism), Ubiquitin-Protein Ligase Complexes (chemistry, 6.3.2.19), Ubiquitin-Protein Ligases (analysis, 6.3.2.19), Xenopus laevis, anaphase-promoting complex (6.3.2.19) |
| Links | PII: S1097-2765(05)01768-5, DOI: 10.1016/j.molcel.2005.11.008, PubMed: 16364912 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1142.map ( map file in CCP4 format, 16385 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | float (32-bit) | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A= B= C: 530.88 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 3.318 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This is a 3D map of the Xenopus APC/C in complex with an activator Cdh1 | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Anaphase Promoting Complex |
|---|---|
| Oligomeric State | Monomer |
| Number of Components | 2 |
| Experimental Mass | 1.5MDa |
| Component #1: protein - Anaphase Promoting Complex | |
| Scientific name | Anaphase Promoting Complex |
| Scientific Name of Species | Xenopus laevis
|
| Common Name of Species | Xenopus |
| NCBI taxonomy | 8355 |
| Recombinant expression | No |
| Component #2: protein - Cdh1 | |
| Scientific name | Cdh1 |
| Oligomeric Details | Monomer |
| Scientific Name of Species | Xenopus laevis |
| Common Name of Species | Xenopus |
| NCBI taxonomy | 8355 |
| Recombinant expression | No |
 Experiment | |
| Sample Preparation | |
| Staining | carbon sandwich with 2% x/v uranyl formate |
|---|---|
| Specimen State | particle |
| Buffer | Details: 20 mM Hepes, 150 mM NaCl, 0.5 mM DTT pH: 7.6 |
| Vitrification | |
| Cryogen Name | NITROGEN |
| Imaging | |
| Microscope | FEI/PHILIPS CM200FEG |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 15 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 90500, Calibrated: 90500 |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder | |
| Holder | Eucentric |
| Model | GATAN LIQUID NITROGEN |
| Camera | |
 Processing | |
| Method | single particle reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | Exact-filter backprojection |
| Software | Imagic-5 |
| CTF Correction | Each particle |
| Resolution By Author | 24 A |
| Resolution Method | FSC at 5sigma |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1142.xml (6.5 KB) | ||
|---|---|---|---|
| Map data | emd_1142.map.gz (14.5 MB) | ||
| Images |  1142.gif (8.5 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1142 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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