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Yorodumi- EMDB-10410: In situ subtomogram average of Chlamydomonas Cdc48 (C6 symmetry) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10410 | |||||||||
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Title | In situ subtomogram average of Chlamydomonas Cdc48 (C6 symmetry) | |||||||||
Map data | In situ subtomogram average of the Chlamydomonas Cdc48 complex (C6 symmetry) | |||||||||
Sample |
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Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 32.8 Å | |||||||||
Authors | Albert S / Schaffer M / Baumeister W / Engel BD | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Direct visualization of degradation microcompartments at the ER membrane. Authors: Sahradha Albert / Wojciech Wietrzynski / Chia-Wei Lee / Miroslava Schaffer / Florian Beck / Jan M Schuller / Patrice A Salomé / Jürgen M Plitzko / Wolfgang Baumeister / Benjamin D Engel / Abstract: To promote the biochemical reactions of life, cells can compartmentalize molecular interaction partners together within separated non-membrane-bound regions. It is unknown whether this strategy is ...To promote the biochemical reactions of life, cells can compartmentalize molecular interaction partners together within separated non-membrane-bound regions. It is unknown whether this strategy is used to facilitate protein degradation at specific locations within the cell. Leveraging in situ cryo-electron tomography to image the native molecular landscape of the unicellular alga , we discovered that the cytosolic protein degradation machinery is concentrated within ∼200-nm foci that contact specialized patches of endoplasmic reticulum (ER) membrane away from the ER-Golgi interface. These non-membrane-bound microcompartments exclude ribosomes and consist of a core of densely clustered 26S proteasomes surrounded by a loose cloud of Cdc48. Active proteasomes in the microcompartments directly engage with putative substrate at the ER membrane, a function canonically assigned to Cdc48. Live-cell fluorescence microscopy revealed that the proteasome clusters are dynamic, with frequent assembly and fusion events. We propose that the microcompartments perform ER-associated degradation, colocalizing the degradation machinery at specific ER hot spots to enable efficient protein quality control. #1: Journal: To Be Published Title: Direct visualization of degradation microcompartments at the ER membrane Authors: Albert S / Wietrzynski W / Lee CW / Schaffer M / Beck F / Schuller JM / Salome PA / Plitzko JM / Baumeister W / Engel BD | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10410.map.gz | 3.1 MB | EMDB map data format | |
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Header (meta data) | emd-10410-v30.xml emd-10410.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10410_fsc.xml | 3.4 KB | Display | FSC data file |
Images | emd_10410.png | 43.8 KB | ||
Others | emd_10410_additional.map.gz | 2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10410 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10410 | HTTPS FTP |
-Validation report
Summary document | emd_10410_validation.pdf.gz | 219.8 KB | Display | EMDB validaton report |
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Full document | emd_10410_full_validation.pdf.gz | 218.9 KB | Display | |
Data in XML | emd_10410_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10410 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10410 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10410.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | In situ subtomogram average of the Chlamydomonas Cdc48 complex (C6 symmetry) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Raw subtomogram average before post-processing (C6 symmetry)
File | emd_10410_additional.map | ||||||||||||
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Annotation | Raw subtomogram average before post-processing (C6 symmetry) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cdc48 inside native Chlamydomonas cells
Entire | Name: Cdc48 inside native Chlamydomonas cells |
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Components |
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-Supramolecule #1: Cdc48 inside native Chlamydomonas cells
Supramolecule | Name: Cdc48 inside native Chlamydomonas cells / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / Location in cell: Cytoplasm |
Molecular weight | Theoretical: 540 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 / Details: TAP media |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV Details: Blotted from the back for 10 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Details | Bidirectional tilt scheme |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 1.5 sec. / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |