+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15364 | |||||||||
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Title | Cryo-EM structure of the SEA complex (consensus map) | |||||||||
Map data | DeepEMhancer sharpened map (wide mask) | |||||||||
Sample |
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Function / homology | Function and homology information urea transport / GATOR1 complex / negative regulation of small GTPase mediated signal transduction / pseudohyphal growth / GATOR2 complex / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / proline transport / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport ...urea transport / GATOR1 complex / negative regulation of small GTPase mediated signal transduction / pseudohyphal growth / GATOR2 complex / Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / proline transport / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / regulation of TORC1 signaling / nuclear pore outer ring / regulation of autophagosome assembly / TORC1 signaling / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / fungal-type vacuole / SUMOylation of RNA binding proteins / fungal-type vacuole membrane / structural constituent of nuclear pore / negative regulation of TOR signaling / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / vacuolar membrane / positive regulation of macroautophagy / positive regulation of TOR signaling / mRNA transport / positive regulation of autophagy / signaling adaptor activity / nuclear pore / ERAD pathway / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / cellular response to amino acid starvation / GTPase activator activity / positive regulation of GTPase activity / meiotic cell cycle / cell periphery / protein import into nucleus / protein transport / nuclear envelope / nuclear membrane / intracellular signal transduction / response to xenobiotic stimulus / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / endoplasmic reticulum / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.95 Å | |||||||||
Authors | Tafur L / Loewith R | |||||||||
Funding support | European Union, 2 items
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Citation | Journal: Nature / Year: 2022 Title: Cryo-EM structure of the SEA complex. Authors: Lucas Tafur / Kerstin Hinterndorfer / Caroline Gabus / Chiara Lamanna / Ariane Bergmann / Yashar Sadian / Farzad Hamdi / Fotis L Kyrilis / Panagiotis L Kastritis / Robbie Loewith / Abstract: The SEA complex (SEAC) is a growth regulator that acts as a GTPase-activating protein (GAP) towards Gtr1, a Rag GTPase that relays nutrient status to the Target of Rapamycin Complex 1 (TORC1) in ...The SEA complex (SEAC) is a growth regulator that acts as a GTPase-activating protein (GAP) towards Gtr1, a Rag GTPase that relays nutrient status to the Target of Rapamycin Complex 1 (TORC1) in yeast. Functionally, the SEAC has been divided into two subcomplexes: SEACIT, which has GAP activity and inhibits TORC1, and SEACAT, which regulates SEACIT. This system is conserved in mammals: the GATOR complex, consisting of GATOR1 (SEACIT) and GATOR2 (SEACAT), transmits amino acid and glucose signals to mTORC1. Despite its importance, the structure of SEAC/GATOR, and thus molecular understanding of its function, is lacking. Here, we solve the cryo-EM structure of the native eight-subunit SEAC. The SEAC has a modular structure in which a COPII-like cage corresponding to SEACAT binds two flexible wings, which correspond to SEACIT. The wings are tethered to the core via Sea3, which forms part of both modules. The GAP mechanism of GATOR1 is conserved in SEACIT, and GAP activity is unaffected by SEACAT in vitro. In vivo, the wings are essential for recruitment of the SEAC to the vacuole, primarily via the EGO complex. Our results indicate that rather than being a direct inhibitor of SEACIT, SEACAT acts as a scaffold for the binding of TORC1 regulators. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15364.map.gz | 926.9 MB | EMDB map data format | |
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Header (meta data) | emd-15364-v30.xml emd-15364.xml | 33.6 KB 33.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15364_fsc.xml | 24 KB | Display | FSC data file |
Images | emd_15364.png | 88.4 KB | ||
Masks | emd_15364_msk_1.map | 1000 MB | Mask map | |
Others | emd_15364_additional_1.map.gz emd_15364_additional_2.map.gz emd_15364_half_map_1.map.gz emd_15364_half_map_2.map.gz | 494.9 MB 884.9 MB 926.6 MB 926.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15364 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15364 | HTTPS FTP |
-Validation report
Summary document | emd_15364_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_15364_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_15364_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | emd_15364_validation.cif.gz | 41.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15364 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15364 | HTTPS FTP |
-Related structure data
Related structure data | 8adlMC 8ae6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15364.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | DeepEMhancer sharpened map (wide mask) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.726 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15364_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_15364_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: DeepEMhancer sharpened map (tight mask)
File | emd_15364_additional_2.map | ||||||||||||
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Annotation | DeepEMhancer sharpened map (tight mask) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15364_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15364_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Seh1-associated complex (SEAC)
+Supramolecule #1: Seh1-associated complex (SEAC)
+Macromolecule #1: Maintenance of telomere capping protein 5
+Macromolecule #2: Nucleoporin SEH1
+Macromolecule #3: SEH-associated protein 4
+Macromolecule #4: Protein transport protein SEC13
+Macromolecule #5: Restriction of telomere capping protein 1
+Macromolecule #6: Nitrogen permease regulator 3
+Macromolecule #7: Vacuolar membrane-associated protein IML1
+Macromolecule #8: Nitrogen permease regulator 2
+Macromolecule #9: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Details | AlphaFold predictions were used as starting models for Sea1, Sea2, Sea3, Sea4, Npr2 and Npr3. Rigid body fit was performed in Chimera, and manual building in Coot. | ||||||
Refinement | Space: REAL / Protocol: AB INITIO MODEL | ||||||
Output model | PDB-8adl: |