EMDB-47278: Human GATOR2 complex - CASTOR1 bound state

Basic information

Entry

Database: EMDB / ID: EMD-47278

• Title: Human GATOR2 complex - CASTOR1 bound state
• Map data: Consensus Map. C2-symmetric

Sample

• Complex: Human GATOR2 complex bound to CASTOR1
  • Protein or peptide: GATOR2 complex protein MIOS
  • Protein or peptide: Nucleoporin SEH1
  • Protein or peptide: Protein SEC13 homolog
  • Protein or peptide: Cytosolic arginine sensor for mTORC1 subunit 1
• Protein or peptide: GATOR2 complex protein WDR24

• Keywords: Signaling protein / nutrient sensor / mTORC1 pathway / stress-responsive protein

Function / homology

Function:

cellular response to L-arginine / molecular sensor activity / Amino acids regulate mTORC1 / arginine binding / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / cellular response to amino acid starvation / protein sequestering activity / identical protein binding / cytosol

Domain/homology:

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 / : / CASTOR, ACT domain / ACT domain / ACT-like domain

Component:

Cytosolic arginine sensor for mTORC1 subunit 1

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.4 Å
• Authors: Wranik M / Rogala KB

Funding support

United States, 5 items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R35 GM150935	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	R00 CA255926	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	P30 CA124435	United States
Department of Defense (DOD, United States)	CA220856	United States
Lustgarten Foundation	1156790	United States

• Citation: Journal: Nature / Year: 2025; Title: Structural basis for the dynamic regulation of mTORC1 by amino acids.; Authors: Max L Valenstein / Maximilian Wranik / Pranav V Lalgudi / Karen Y Linde-Garelli / Yuri Choi / Raghu R Chivukula / David M Sabatini / Kacper B Rogala / ; Abstract: The mechanistic target of rapamycin complex 1 (mTORC1) anchors a conserved signalling pathway that regulates growth in response to nutrient availability. Amino acids activate mTORC1 through the Rag GTPases, which are regulated by GATOR, a supercomplex consisting of GATOR1, KICSTOR and the nutrient-sensing hub GATOR2 (refs. ). GATOR2 forms an octagonal cage, with its distinct WD40 domain β-propellers interacting with GATOR1 and the leucine sensors Sestrin1 and Sestrin2 (SESN1 and SESN2) and the arginine sensor CASTOR1 (ref. ). The mechanisms through which these sensors regulate GATOR2 and how they detach from it upon binding their cognate amino acids remain unknown. Here, using cryo-electron microscopy, we determined the structures of a stabilized GATOR2 bound to either Sestrin2 or CASTOR1. The sensors occupy distinct and non-overlapping binding sites, disruption of which selectively impairs the ability of mTORC1 to sense individual amino acids. We also resolved the apo (leucine-free) structure of Sestrin2 and characterized the amino acid-induced structural rearrangements within Sestrin2 and CASTOR1 that trigger their dissociation from GATOR2. Binding of either sensor restricts the dynamic WDR24 β-propeller of GATOR2, a domain essential for nutrient-dependent mTORC1 activation. These findings reveal the allosteric mechanisms that convey amino acid sufficiency to GATOR2 and the ensuing structural changes that lead to mTORC1 activation.

History

Deposition	Oct 10, 2024	-
Header (metadata) release	May 20, 2026	-
Map release	May 20, 2026	-
Update	May 20, 2026	-
Current status	May 20, 2026	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_47278.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: Consensus Map. C2-symmetric
• Voxel size: X=Y=Z: 0.8697 Å

Density

Contour Level	By AUTHOR: 0.05
Minimum - Maximum	-0.2021295 - 0.5666755
Average (Standard dev.)	0.0016488818 (±0.015373601)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 480 480 480 Spacing 480 480 480
Cell	A=B=C: 417.456 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_47278_msk_1.map

Mask #2

• File: emd_47278_msk_2.map

Mask #3

• File: emd_47278_msk_3.map

Mask #4

• File: emd_47278_msk_4.map

Mask #5

• File: emd_47278_msk_5.map

Additional map: Composite Map. Half Map 1

• File: emd_47278_additional_1.map
• Annotation: Composite Map. Half Map 1

Additional map: Local Map 2. Sharpened

• File: emd_47278_additional_10.map
• Annotation: Local Map 2. Sharpened

Additional map: Local Map 2. Unsharpened

• File: emd_47278_additional_11.map
• Annotation: Local Map 2. Unsharpened

Additional map: Local Map 2. Half Map 2

• File: emd_47278_additional_12.map
• Annotation: Local Map 2. Half Map 2

Additional map: Local Map 3. Half Map 1

• File: emd_47278_additional_13.map
• Annotation: Local Map 3. Half Map 1

Additional map: Local Map 3. Sharpened

• File: emd_47278_additional_14.map
• Annotation: Local Map 3. Sharpened

Additional map: Local Map 3. Half Map 2

• File: emd_47278_additional_15.map
• Annotation: Local Map 3. Half Map 2

Additional map: Local Mal 3. Unsharpened

• File: emd_47278_additional_16.map
• Annotation: Local Mal 3. Unsharpened

Additional map: Local Map 4. Sharpened

• File: emd_47278_additional_17.map
• Annotation: Local Map 4. Sharpened

Additional map: Local Map 4. Half Map 2

• File: emd_47278_additional_18.map
• Annotation: Local Map 4. Half Map 2

Additional map: Local Map 4. Half Map 1

• File: emd_47278_additional_19.map
• Annotation: Local Map 4. Half Map 1

Additional map: Composite Map. Unsharpened. C2-symmetric

• File: emd_47278_additional_2.map
• Annotation: Composite Map. Unsharpened. C2-symmetric

Additional map: Local Map 4. Unsharpened

• File: emd_47278_additional_20.map
• Annotation: Local Map 4. Unsharpened

Additional map: Local Map 1. Half Map 2

• File: emd_47278_additional_21.map
• Annotation: Local Map 1. Half Map 2

Additional map: Local Map 1. Half Map 1

• File: emd_47278_additional_22.map
• Annotation: Local Map 1. Half Map 1

Additional map: Local Map 5. Sharpened

• File: emd_47278_additional_23.map
• Annotation: Local Map 5. Sharpened

Additional map: Local Map 5. Unsharpened

• File: emd_47278_additional_24.map
• Annotation: Local Map 5. Unsharpened

Additional map: Composite Map. Half Map 2

• File: emd_47278_additional_3.map
• Annotation: Composite Map. Half Map 2

Additional map: Composite Map. Sharpened. C2-symmetric

• File: emd_47278_additional_4.map
• Annotation: Composite Map. Sharpened. C2-symmetric

Additional map: Local Map 1. Half Map 1

• File: emd_47278_additional_5.map
• Annotation: Local Map 1. Half Map 1

Additional map: Local Map 1. Half Map 2

• File: emd_47278_additional_6.map
• Annotation: Local Map 1. Half Map 2

Additional map: Local Map 1. Sharpened

• File: emd_47278_additional_7.map
• Annotation: Local Map 1. Sharpened

Additional map: Local Map 1. Unsharpened

• File: emd_47278_additional_8.map
• Annotation: Local Map 1. Unsharpened

Additional map: Local Map 2. Half Map 1

• File: emd_47278_additional_9.map
• Annotation: Local Map 2. Half Map 1

Half map: Consensus Map. Half Map 2

• File: emd_47278_half_map_1.map
• Annotation: Consensus Map. Half Map 2

Half map: Consensus Map. Half Map 1

• File: emd_47278_half_map_2.map
• Annotation: Consensus Map. Half Map 1

Sample components

Entire : Human GATOR2 complex bound to CASTOR1

• Entire: Name: Human GATOR2 complex bound to CASTOR1

Components

• Complex: Human GATOR2 complex bound to CASTOR1
  • Protein or peptide: GATOR2 complex protein MIOS
  • Protein or peptide: Nucleoporin SEH1
  • Protein or peptide: Protein SEC13 homolog
  • Protein or peptide: Cytosolic arginine sensor for mTORC1 subunit 1
• Protein or peptide: GATOR2 complex protein WDR24

Supramolecule #1: Human GATOR2 complex bound to CASTOR1

• Supramolecule: Name: Human GATOR2 complex bound to CASTOR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 1.3 MDa

Macromolecule #1: GATOR2 complex protein MIOS

• Macromolecule: Name: GATOR2 complex protein MIOS / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 88.740953 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

ERISLAWSPI TSLMWACGRH LYECTEMFVA RSIAADHKDL IHDVSFDFHG RRMATCSSDQ SVKVWDKSES GDWHCTASWK THSGSVWRV TWAHPEFGQV LASCSFDRTA AVWEEIVGES NDKLRGQSHW VKRTTLVDSR TSVTDVKFAP KHMGLMLATC S ADGIVRIY EAPDVMNLSQ WSLQHEISCK LSCSCISWNP SSSRAHSPMI AVGSDDSSPN AMAKVQIFEY NENTRKYAKA ET LMTVTDP VHDIAFAPNL GRSFHILAIA TKDVRIFTLK PVRKELTSSG GPTKFEIHIV AQFDNHNSQV WRVSWNITGT VLA SSGDDG CVRLWKANYM DNWKCTGILK GNGSPVEKDI ATKMRLRALS RYGLDTEQVW RNHILAGNED PQLKSLWYTL HFMK QYTED MDQKSPGNKG SLVYAGIKSI VKSSLGMVES SRHNWSGDIQ NLNEERILAL QLCGWIKKGT DVDVGPFLNS LVQEG EWER AAAVALFNLD IRRAIQILNE GASSEKGDLN LNVVAMALSG YTDEKNSLWR EMCSTLRLQL NNPYLCVMFA FLTSET GSY DGVLYENKVA VRDRVAFACK FLSDTQLNRY IEKLTNEMKE AGNLEGILLT GLTKDGVDLM ESYVDRTGDV QTASYCM LQ GSPLDVLKDE RVQYWIENYR NLLDAWRFWH KRAEFDIHRS KLDPSSKPLA QVFVSCNFCG KSISYSKVTS CPGCRKPL P RCALCLINMG TPVSKDKKLA QFNNWFTWCH NCRHGGHAGH MLSWFRDHAE CPVSACTCKC MQLDT

Macromolecule #2: Nucleoporin SEH1

• Macromolecule: Name: Nucleoporin SEH1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 63.832641 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

AAKESLVAEP FAGLASSALS VFETEPMFVA RSIAADHKDL IHDVSFDFHG RRMATCSSDQ SVKVWDKSES GDWHCTASWK THSGSVWRV TWAHPEFGQV LASCSFDRTA AVWEEIVSHW VKRTTLVDSR TSVTDVKFAP KHMGLMLATC SADGIVRIYE A PDVMNLSQ WSLQHEISCK LSCSCISWNP SSSRAHSPMI AVGSDDSSPN AMAKVQIFEY NENTRKYAKA ETLMTVTDPV HD IAFAPNL GRSFHILAIA TKDVRIFTLK PVRKELTSSG GPTKFEIHIV AQFDNHNSQV WRVSWNITGT VLASSGDDGC VRL WKANYM DNWKCTGILK GGGMRWFVDT AERYALAGRP LAELCDHNAK VARELGRNQV AQTWTMLRII YCSPSSSFSL LSVS HALYD SRLPPDFFGV LVRDMLHFYA EQGDVQMAVS VLIVLGERVR KDIDEQTQEH WYTSYIDLLQ RFRLWNVSNE VVKLS TSRA VSCLNQASTT LHVNCSHCKR PMSSRGWVCD RCHRCASMCA VCHHVVKGLF VWCQGCSHGG HLQHIMKWLE GSSHCP AGC GHLCEYS

Macromolecule #3: Protein SEC13 homolog

• Macromolecule: Name: Protein SEC13 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 60.774332 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

AYGSYQDANI PFPRTSGARF CGAGYLVYFT RPMTMHRAVS PTEPTPRSLS ALSAYHTKRE GSDSGNRQIK AAGKVIIQDG SGSGMVSVI NTVDTSHEDM IHDAQMDYYG TRLATCSSDR SVKIFDVRNG GQILIADLRG HEGPVWQVAW AHPMYGNILA S CSYDRKVI IWREENGTWE KSHEHAGHDS SVNSVCWAPH DYGLILACGS SDGAISLLTY TGEGQWEVKK INNAHTIGCN AV SWAPAVV PGSLIDHPSG QKPNYIKRFA SGGCDNLIKL WKEEEDGQWK EEQKLEAHSD WVRDVAWAPS IGLPTSTIAS CSQ DGRVFI WTCDDASSNT WSPKLLHKFN DVVWHVSWSI TANILAVSGG DNKVTLWKES VDGQWVCISI ACLLPVHKSL GELY ILNVN DIQETCQKNA ASALLVGRKD LVQVWSLATV ATDLCLGPKS DPDLETPWAR HPFGRQLLES LLAHYCRLRD VQTLA MLCS VFEAQSLDPR ERERDQHDKN KRLLDPANTQ QFDDFKKCYG EILYRWGLRE KRAEVLKFVS C

Macromolecule #4: Cytosolic arginine sensor for mTORC1 subunit 1

• Macromolecule: Name: Cytosolic arginine sensor for mTORC1 subunit 1 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 36.222164 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

MELHILEHRV RVLSVARPGL WLYTHPLIKL LFLPRRSRCK FFSLTETPED YTLMVDEEGF KELPPSEFLQ VAEATWLVLN VSSHSGAAV QAAGVTKIAR SVIAPLAEHH VSVLMLSTYQ TDFILVREQD LSVVIHTLAQ EFDIYREVGG EPVPVTRDDS S NGFPRTQH GPSPTVHPIQ SPQNRFCVLT LDPETLPAIA TTLIDVLFYS HSTPKEAASS SPEPSSITFF AFSLIEGYIS IV MDAETQK KFPSDLLLTS SSGELWRMVR IGGQPLGFDE CGIVAQIAGP LAAADISAYY ISTFNFDHAL VPEDGIGSVI EVL QRRQEG LA

UniProtKB: Cytosolic arginine sensor for mTORC1 subunit 1

Macromolecule #5: GATOR2 complex protein WDR24

• Macromolecule: Name: GATOR2 complex protein WDR24 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 118.434242 KDa
• Recombinant expression: Organism: Homo sapiens (human)

Sequence

String:

TKPDILWAPH HVDRFVVCDS ELSLYHVEST VNSELKAGSL RLSEDSAATL LSINSDTPYM KCVAWYLNYD PECLLAVGEA NGRVVLTSL GQDHNSKFKD LIGKEYVPKH ARQCNTLAWN PLDSDWLAAG LDKHRADFSV LIWDICLLTK PLYELGQNDA C LSLCWLPR DQKLLLAGMH RNLAIFDLRN TSEKMFVNTK AVQGVTVDPY FHDRVASFYE GQVAIWDLRK FEKPVLTLTE QP KPLTKVA WCPTRTGLLA TLTRDSNIIR LYDMQHTPTP IGPTIIERSV QPCDNYIASF AWHPTSQNRM IVVTPNRTMS DFT VFTKPD ILWAPHHVDR FVVCDSELSL YHVESTVNSE LKAGSLRLSE DSAATLLSIN SDTPYMKCVA WYLNYDPECL LAVG QANGR VVLTSLGQDH NSKFKDLIGK EFVPKHARQC NTLAWNPLDS NWLAAGLDKH RADFSVLIWD ICLVTKPLYE LGQND ACLS LCWLPRDQKL LLAGMHRNLA IFDLRNTSQK MFVNTKAVQG VTVDPYFHDR VASFYEGQVA IWDLRKFEKP VLTLTE QPK PLTKVAWCPT RTGLLATLTR DSNIIRLYDM QHTIIERSVQ PCDDYIASFA WHPTSQNRMI VVTPNRTMSD FTVFVLT GR TMHCHLDAPA NAISVCRDAA QVVVAGRSIF KIYAIEEEQF VEKLNLRVGR KPSLNLSCAD VVWHQMDENL LATAATNG V VVTWNLGRPS RNKQDQLFTE HKRTVNKVCF HPTEAHVLLS GSQDGFMKCF DLRRKDSVST FSGQSESVRD VQFSIRDYF TFASTFENGN VQLWDIRRPD RCERMFTAHN GPVFCCDWHP EDRGWLATGG RDKMVKVWDM TTHRAKEMHC VQTIASVARV KWRPECRHH LATCSMMVDH NIYVWDVRRP FVPAAMFEEH RDVTTGIAWR HPHDPSFLLS GSKDSSLCQH LFRDASQPVE R ANPEGLCY GLFGDLAFPP FGVYCSHCRS TFQCAICHVA VRGSSNFCLT CGHGGHTSHM MEWFRTQEVC PTGCGCHCLL ES TF

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.4
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 69.44 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

Startup model

Type of model: PDB ENTRY
PDB model - PDB ID:

7uhy

• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 865410
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD