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Yorodumi- EMDB-12222: tomogram of membrane tubules coated with metazoan retromer:SNX3 i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12222 | ||||||||||||||||||
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Title | tomogram of membrane tubules coated with metazoan retromer:SNX3 in the presence of Wls cargo. | ||||||||||||||||||
Map data | representative tomogram of metazoan retromer:SNX3:Wls | ||||||||||||||||||
Sample |
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Biological species | Mus musculus (house mouse) | ||||||||||||||||||
Method | electron tomography / cryo EM | ||||||||||||||||||
Authors | Leneva N / Kovtun O / Morado DR / Briggs JAG / Owen DJ | ||||||||||||||||||
Funding support | United Kingdom, 5 items
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Citation | Journal: Sci Adv / Year: 2021 Title: Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly. Authors: Natalya Leneva / Oleksiy Kovtun / Dustin R Morado / John A G Briggs / David J Owen / Abstract: Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core ...Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core (VPS26/VPS29/VPS35) is present on cargo-transporting, tubular carriers along with a range of sorting nexins. Here, we elucidate the structural basis of membrane tubulation and coupled cargo recognition by metazoan and fungal retromer coats assembled with the non-Bin1/Amphiphysin/Rvs (BAR) sorting nexin SNX3 using cryo-electron tomography. The retromer core retains its arched, scaffolding structure but changes its mode of membrane recruitment when assembled with different SNX adaptors, allowing cargo recognition at subunit interfaces. Thus, membrane bending and cargo incorporation can be modulated to allow retromer to traffic cargoes along different cellular transport routes. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12222.map.gz | 528.4 MB | EMDB map data format | |
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Header (meta data) | emd-12222-v30.xml emd-12222.xml | 8.7 KB 8.7 KB | Display Display | EMDB header |
Images | emd_12222.png | 139.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12222 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12222 | HTTPS FTP |
-Validation report
Summary document | emd_12222_validation.pdf.gz | 154.9 KB | Display | EMDB validaton report |
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Full document | emd_12222_full_validation.pdf.gz | 154 KB | Display | |
Data in XML | emd_12222_validation.xml.gz | 4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12222 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12222 | HTTPS FTP |
-Related structure data
Related structure data | 7blnC 7bloC 7blpC 7blqC 7blrC C: citing same article (ref.) |
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EM raw data | EMPIAR-10633 (Title: Cryo-electron tomography of the metazoan membrane-assembled retromer:SNX3 coat containing Wls cargo motif Data size: 764.9 Data #1: Raw image frames for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes [micrographs - multiframe] Data #2: Corrected, aligned and order-sorted tilt series for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes [tilt series] Data #3: Corrected, aligned, dose-filtered and order-sorted tilt series for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12222.map.gz / Format: CCP4 / Size: 702.4 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | representative tomogram of metazoan retromer:SNX3:Wls | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.804 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : membrane tubules coated with metazoan retromer:SNX3 complex.
Entire | Name: membrane tubules coated with metazoan retromer:SNX3 complex. |
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Components |
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-Supramolecule #1: membrane tubules coated with metazoan retromer:SNX3 complex.
Supramolecule | Name: membrane tubules coated with metazoan retromer:SNX3 complex. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: metazoan retromer:SNX3 complex assembled on liposomes containing Wls cargo. |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: BBI Solutions / Diameter: 5 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number images used: 41 |
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