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Yorodumi- EMDB-16485: Cryo-EM structure of the yeast SPT-Orm1-Dimer complex, local refi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16485 | |||||||||
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Title | Cryo-EM structure of the yeast SPT-Orm1-Dimer complex, local refinement of a monomer | |||||||||
Map data | map-main | |||||||||
Sample |
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Keywords | Serine-Palmitoyl-Transferase / SPT / Orm-Protein / TRANSFERASE | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Schaefer J / Koerner C / Parey K / Januliene D / Moeller A / Froehlich F | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure of the ceramide-bound SPOTS complex. Authors: Jan-Hannes Schäfer / Carolin Körner / Bianca M Esch / Sergej Limar / Kristian Parey / Stefan Walter / Dovile Januliene / Arne Moeller / Florian Fröhlich / Abstract: Sphingolipids are structural membrane components that also function in cellular stress responses. The serine palmitoyltransferase (SPT) catalyzes the rate-limiting step in sphingolipid biogenesis. ...Sphingolipids are structural membrane components that also function in cellular stress responses. The serine palmitoyltransferase (SPT) catalyzes the rate-limiting step in sphingolipid biogenesis. Its activity is tightly regulated through multiple binding partners, including Tsc3, Orm proteins, ceramides, and the phosphatidylinositol-4-phosphate (PI4P) phosphatase Sac1. The structural organization and regulatory mechanisms of this complex are not yet understood. Here, we report the high-resolution cryo-EM structures of the yeast SPT in complex with Tsc3 and Orm1 (SPOT) as dimers and monomers and a monomeric complex further carrying Sac1 (SPOTS). In all complexes, the tight interaction of the downstream metabolite ceramide and Orm1 reveals the ceramide-dependent inhibition. Additionally, observation of ceramide and ergosterol binding suggests a co-regulation of sphingolipid biogenesis and sterol metabolism within the SPOTS complex. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16485.map.gz | 203.8 MB | EMDB map data format | |
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Header (meta data) | emd-16485-v30.xml emd-16485.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16485_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_16485.png | 74 KB | ||
Masks | emd_16485_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-16485.cif.gz | 4.3 KB | ||
Others | emd_16485_half_map_1.map.gz emd_16485_half_map_2.map.gz | 200.7 MB 200.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16485 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16485 | HTTPS FTP |
-Validation report
Summary document | emd_16485_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_16485_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_16485_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_16485_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16485 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16485 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16485.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | map-main | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.924 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16485_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Dimer-Map-Masked-Half-A
File | emd_16485_half_map_1.map | ||||||||||||
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Annotation | Dimer-Map-Masked-Half-A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Dimer-Map-Masked-Half-B
File | emd_16485_half_map_2.map | ||||||||||||
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Annotation | Dimer-Map-Masked-Half-B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Heterotetrameric complex of Orm1 with Lcb1, Lcb2 and Tsc3
Entire | Name: Heterotetrameric complex of Orm1 with Lcb1, Lcb2 and Tsc3 |
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Components |
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-Supramolecule #1: Heterotetrameric complex of Orm1 with Lcb1, Lcb2 and Tsc3
Supramolecule | Name: Heterotetrameric complex of Orm1 with Lcb1, Lcb2 and Tsc3 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 180 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10.0 mg/mL |
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Buffer | pH: 6.8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Specialist optics | Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 13604 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 13000 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 86 |
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