+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20138 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cdc48 Symmetric Hexamer | |||||||||
Map data | Cdc48 Symmetric Hexamer | |||||||||
Sample |
| |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Cooney I / Han H / Hill CP / Shen PS | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Science / Year: 2019 Title: Structure of the Cdc48 segregase in the act of unfolding an authentic substrate. Authors: Ian Cooney / Han Han / Michael G Stewart / Richard H Carson / Daniel T Hansen / Janet H Iwasa / John C Price / Christopher P Hill / Peter S Shen / Abstract: The cellular machine Cdc48 functions in multiple biological pathways by segregating its protein substrates from a variety of stable environments such as organelles or multi-subunit complexes. Despite ...The cellular machine Cdc48 functions in multiple biological pathways by segregating its protein substrates from a variety of stable environments such as organelles or multi-subunit complexes. Despite extensive studies, the mechanism of Cdc48 has remained obscure, and its reported structures are inconsistent with models of substrate translocation proposed for other AAA+ ATPases (adenosine triphosphatases). Here, we report a 3.7-angstrom-resolution structure of Cdc48 in complex with an adaptor protein and a native substrate. Cdc48 engages substrate by adopting a helical configuration of substrate-binding residues that extends through the central pore of both of the ATPase rings. These findings indicate a unified hand-over-hand mechanism of protein translocation by Cdc48 and other AAA+ ATPases. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20138.map.gz | 5.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-20138-v30.xml emd-20138.xml | 8.7 KB 8.7 KB | Display Display | EMDB header |
Images | emd_20138.png | 111.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20138 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20138 | HTTPS FTP |
-Validation report
Summary document | emd_20138_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_20138_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_20138_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20138 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20138 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_20138.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cdc48 Symmetric Hexamer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.168 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Cdc48-Substrate Complex
Entire | Name: Cdc48-Substrate Complex |
---|---|
Components |
|
-Supramolecule #1: Cdc48-Substrate Complex
Supramolecule | Name: Cdc48-Substrate Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: ab initio |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26203 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |