- EMDB-15364: Cryo-EM structure of the SEA complex (consensus map) -
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Basic information
Entry
Database: EMDB / ID: EMD-15364
Title
Cryo-EM structure of the SEA complex (consensus map)
Map data
DeepEMhancer sharpened map (wide mask)
Sample
Complex: Seh1-associated complex (SEAC)
Protein or peptide: Maintenance of telomere capping protein 5
Protein or peptide: Nucleoporin SEH1
Protein or peptide: SEH-associated protein 4
Protein or peptide: Protein transport protein SEC13
Protein or peptide: Restriction of telomere capping protein 1
Protein or peptide: Nitrogen permease regulator 3
Protein or peptide: Vacuolar membrane-associated protein IML1
Protein or peptide: Nitrogen permease regulator 2
Ligand: ZINC ION
Keywords
GTPase activating protein / coatomer / TOR signaling / SIGNALING PROTEIN
Function / homology
Function and homology information
urea transport / GATOR1 complex / negative regulation of small GTPase mediated signal transduction / GATOR2 complex / pseudohyphal growth / 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 / GATOR2 complex / pseudohyphal growth / 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 / COPII vesicle coat / TORC1 signaling / 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 / regulation of autophagosome assembly / SUMOylation of SUMOylation proteins / fungal-type vacuole / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / negative regulation of TOR signaling / cellular response to nitrogen starvation / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / vacuolar membrane / fungal-type vacuole membrane / positive regulation of macroautophagy / positive regulation of TOR signaling / mRNA transport / meiotic cell cycle / positive regulation of autophagy / nuclear pore / signaling adaptor activity / ERAD pathway / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / cellular response to amino acid starvation / GTPase activator activity / cell periphery / protein import into nucleus / nuclear envelope / protein transport / cellular response to oxidative stress / nuclear membrane / intracellular signal transduction / response to xenobiotic stimulus / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / metal ion binding / cytoplasm / cytosol Similarity search - Function
WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / : / : / Zinc-ribbon like family / RING/Ubox like zinc-binding domain / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1 ...WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / : / : / Zinc-ribbon like family / RING/Ubox like zinc-binding domain / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1 / : / Nitrogen Permease regulator of amino acid transport activity 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1, N-terminal domain / RWD domain / RWD domain / RWD domain profile. / RWD / Sec13/Seh1 family / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily Similarity search - Domain/homology
SEH-associated protein 4 / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein IML1 / Nucleoporin SEH1 / Maintenance of telomere capping protein 5 / Protein transport protein SEC13 / Restriction of telomere capping protein 1 Similarity search - Component
Biological species
Saccharomyces cerevisiae (brewer's yeast)
Method
single particle reconstruction / cryo EM / Resolution: 2.95 Å
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.
chain_id: A, source_name: PDB, initial_model_type: experimental model
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.
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