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- PDB-9oti: GATOR2 complex bound to arginine sensor CASTOR1 -

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Basic information

Entry
Database: PDB / ID: 9oti
TitleGATOR2 complex bound to arginine sensor CASTOR1
Components
  • (GATOR complex protein ...) x 2
  • Cytosolic arginine sensor for mTORC1 subunit 1
  • GATOR2 complex protein MIOS
  • Nucleoporin SEH1
  • Protein SEC13 homolog
KeywordsSIGNALING PROTEIN / Complex / mTORC1 / Signaling / Nutrients / Amino Acid Sensing
Function / homology
Function and homology information


oligodendrocyte progenitor proliferation / GATOR2 complex / cellular response to L-arginine / molecular sensor activity / Seh1-associated complex / COPII-coated vesicle budding / protein exit from endoplasmic reticulum / positive regulation of ER to Golgi vesicle-mediated transport / nuclear pore outer ring / nuclear pore organization ...oligodendrocyte progenitor proliferation / GATOR2 complex / cellular response to L-arginine / molecular sensor activity / Seh1-associated complex / COPII-coated vesicle budding / protein exit from endoplasmic reticulum / positive regulation of ER to Golgi vesicle-mediated transport / nuclear pore outer ring / nuclear pore organization / COPII-coated vesicle cargo loading / central nervous system myelin formation / COPII vesicle coat / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / positive regulation of protein exit from endoplasmic reticulum / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Amino acids regulate mTORC1 / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / NS1 Mediated Effects on Host Pathways / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / protein K6-linked ubiquitination / Transport of Mature mRNA derived from an Intron-Containing Transcript / oligodendrocyte differentiation / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / arginine binding / COPII-mediated vesicle transport / protein-containing complex localization / vacuolar membrane / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / positive regulation of macroautophagy / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mitotic metaphase chromosome alignment / positive regulation of TOR signaling / mRNA transport / SUMOylation of DNA damage response and repair proteins / negative regulation of TORC1 signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of TORC1 signaling / MHC class II antigen presentation / signaling adaptor activity / cellular response to nutrient levels / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cellular response to amino acid starvation / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / protein localization to plasma membrane / regulation of autophagy / HCMV Late Events / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / protein sequestering activity / ER to Golgi transport vesicle membrane / RHO GTPases Activate Formins / protein import into nucleus / intracellular protein transport / RING-type E3 ubiquitin transferase / ISG15 antiviral mechanism / kinetochore / autophagy / HCMV Early Events / Separation of Sister Chromatids / ubiquitin protein ligase activity / nuclear envelope / protein transport / snRNP Assembly / cell division / lysosomal membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / extracellular exosome / nucleoplasm / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
WDR59, modified RING finger, H2 subclass (C3H3C2-type) / MIOS, WD40 repeat / WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / : / Zinc-ribbon like family / MIOS, alpha-solenoid / CASTOR family / CASTOR1, N-terminal ...WDR59, modified RING finger, H2 subclass (C3H3C2-type) / MIOS, WD40 repeat / WD repeat protein mio, zinc-ribbon like domain / GATOR complex protein WDR24 / MIOS/Sea4 / : / Zinc-ribbon like family / MIOS, alpha-solenoid / CASTOR family / CASTOR1, N-terminal / : / Cytosolic arginine sensor for mTORC1 subunit 1 N-terminal domain / Cytosolic arginine sensor for mTORC1 subunit 1/2, ACT-like / : / : / : / RING/Ubox like zinc-binding domain / CASTOR, ACT domain / ACT domain / RWD domain profile. / RWD / RWD domain / Sec13/Seh1 family / : / Nucleolar protein 10-like, N-terminal domain / ACT-like domain / Ubiquitin-conjugating enzyme/RWD-like / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Protein SEC13 homolog / GATOR2 complex protein WDR59 / Cytosolic arginine sensor for mTORC1 subunit 1 / Nucleoporin SEH1 / GATOR2 complex protein WDR24 / GATOR2 complex protein MIOS
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsJansen, R.M. / Hurley, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA285366 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis for mTORC1 regulation by the CASTOR1-GATOR2 complex.
Authors: Rachel M Jansen / Clément Maghe / Karla Tapia / Selina Wu / Serim Yang / Xuefeng Ren / Roberto Zoncu / James H Hurley /
Abstract: Mechanistic target of rapamycin complex 1 (mTORC1) is a nutrient-responsive master regulator of metabolism. Amino acids control the recruitment and activation of mTORC1 at the lysosome through the ...Mechanistic target of rapamycin complex 1 (mTORC1) is a nutrient-responsive master regulator of metabolism. Amino acids control the recruitment and activation of mTORC1 at the lysosome through the nucleotide loading state of the heterodimeric Rag GTPases. Under low nutrients, including arginine, the GTPase-activating protein complex GATOR1 promotes GTP hydrolysis on RagA/B, inactivating mTORC1. GATOR1 is regulated by the cage-like GATOR2 complex and cytosolic amino acid sensors. To understand how the arginine sensor CASTOR1 binds to GATOR2 to disinhibit GATOR1 under low cytosolic arginine, we determined the cryo-electron microscopy structure of human GATOR2 bound to CASTOR1 in the absence of arginine. Two MIOS WD40 domain β-propellers of the GATOR2 cage engage with both subunits of a single CASTOR1 homodimer. Each propeller binds to a negatively charged MIOS-binding interface on CASTOR1 that is distal to the arginine pocket. The structure shows how arginine-triggered loop ordering in CASTOR1 blocks the MIOS-binding interface, switches off its binding to GATOR2 and, thus, communicates to downstream mTORC1 activation.
History
DepositionMay 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GATOR2 complex protein MIOS
B: GATOR2 complex protein MIOS
C: GATOR complex protein WDR24
D: GATOR complex protein WDR59
E: Nucleoporin SEH1
F: Nucleoporin SEH1
G: Nucleoporin SEH1
H: Protein SEC13 homolog
L: GATOR2 complex protein MIOS
M: GATOR complex protein WDR24
N: GATOR complex protein WDR59
O: Nucleoporin SEH1
P: Nucleoporin SEH1
Q: Nucleoporin SEH1
R: Protein SEC13 homolog
T: GATOR2 complex protein MIOS
U: Cytosolic arginine sensor for mTORC1 subunit 1
V: Cytosolic arginine sensor for mTORC1 subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,175,08847
Polymers1,173,19118
Non-polymers1,89729
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 14 molecules ABLTEFGOPQHRUV

#1: Protein
GATOR2 complex protein MIOS / Missing oocyte meiosis regulator homolog


Mass: 98700.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MIOS / Production host: Homo sapiens (human) / References: UniProt: Q9NXC5
#4: Protein
Nucleoporin SEH1 / GATOR2 complex protein SEH1 / Nup107-160 subcomplex subunit SEH1 / SEC13-like protein


Mass: 39700.566 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEH1L, SEC13L, SEH1 / Production host: Homo sapiens (human) / References: UniProt: Q96EE3
#5: Protein Protein SEC13 homolog / GATOR complex protein SEC13 / SEC13-like protein 1 / SEC13-related protein


Mass: 35578.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SEC13, D3S1231E, SEC13A, SEC13L1, SEC13R / Production host: Homo sapiens (human) / References: UniProt: P55735
#6: Protein Cytosolic arginine sensor for mTORC1 subunit 1 / Cellular arginine sensor for mTORC1 protein 1 / GATS-like protein 3


Mass: 36249.238 Da / Num. of mol.: 2 / Mutation: D304A, S111A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASTOR1, GATSL3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WTX7

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GATOR complex protein ... , 2 types, 4 molecules CMDN

#2: Protein GATOR complex protein WDR24 / WD repeat-containing protein 24


Mass: 88326.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR24, C16orf21, JFP7 / Production host: Homo sapiens (human) / References: UniProt: Q96S15
#3: Protein GATOR complex protein WDR59 / WD repeat-containing protein 59


Mass: 109938.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR59, KIAA1923, FP977 / Production host: Homo sapiens (human) / References: UniProt: Q6PJI9

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Non-polymers , 1 types, 29 molecules

#7: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1GATOR2 complex bound to arginine sensor CASTOR1COMPLEX#1-#60MULTIPLE SOURCES
2GATOR2 ComplexCOMPLEX#2-#5, #11RECOMBINANT
3CASTOR1COMPLEX#61RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.3.1particle selection
4cryoSPARCv3.3.1CTF correction
10cryoSPARCv3.3.1initial Euler assignment
11cryoSPARCv3.3.1final Euler assignment
12cryoSPARCv3.3.1classification
13cryoSPARCv3.3.13D reconstruction
Image processingDetails: Raw movies were imported into cryosparc2 v4.3.1 39. Patch Motion Corr. was used for motion correction and Patch CTF estimated (multi) was used for CTF determination.
CTF correctionDetails: Patch Motion Corr. was used for motion correction and Patch CTF estimated (multi) was used for CTF determination.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2289288
Details: Cryosparc blob picker with a diameter range of 200 A-280 A was used to generate 3,467,659 which was inspected to trim the particle set to 2,289,288 particles. Particles were extracted with a ...Details: Cryosparc blob picker with a diameter range of 200 A-280 A was used to generate 3,467,659 which was inspected to trim the particle set to 2,289,288 particles. Particles were extracted with a box size of 560x560 pixels in cryosparc2.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140606 / Algorithm: BACK PROJECTION
Details: The final particle set contained 140,606 particles and a round of homogenous refinement resulted in a 3.89 A map at 0.143 FSC.
Num. of class averages: 1 / Symmetry type: POINT

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