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- EMDB-47276: Human GATOR2 complex - apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-47276
TitleHuman GATOR2 complex - apo state
Map dataConsensus Map. C2-symmetric
Sample
  • Complex: Human GATOR2 Complex - Apo State
    • Protein or peptide: GATOR2 complex protein MIOS
    • Protein or peptide: GATOR2 complex protein WDR24
    • Protein or peptide: Protein SEC13 homolog
KeywordsSignaling protein / nutrient sensor / mTORC1 pathway
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsWranik M / Rogala KB
Funding support United States, 5 items
OrganizationGrant numberCountry
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 Foundation1156790 United States
CitationJournal: 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 ...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
DepositionOct 10, 2024-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47276.png

Downloads & links

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Map

FileDownload / File: emd_47276.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus Map. C2-symmetric
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 480 pix.
= 417.456 Å		0.87 Å/pix.
x 480 pix.
= 417.456 Å		0.87 Å/pix.
x 480 pix.
= 417.456 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8697 Å
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Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.15350884 - 0.43159655
Average (Standard dev.)0.00094910513 (±0.010904635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 417.456 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47276_msk_1.map
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Mask #2

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Additional map: Composite Map. Half Map 1

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Additional map: Local Map 1. Sharpened

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AnnotationLocal Map 1. Sharpened
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Additional map: Local Map 2. Sharpened

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AnnotationLocal Map 2. Sharpened
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Additional map: Local Map 2. Half Map 2

Fileemd_47276_additional_12.map
AnnotationLocal Map 2. Half Map 2
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Additional map: Local Map 3. Half Map 2

Fileemd_47276_additional_13.map
AnnotationLocal Map 3. Half Map 2
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Additional map: Local Map 3. Sharpened

Fileemd_47276_additional_14.map
AnnotationLocal Map 3. Sharpened
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Additional map: Local Map 3. Half Map 1

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AnnotationLocal Map 3. Half Map 1
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Additional map: Local Map 3. Unsharpened

Fileemd_47276_additional_16.map
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Additional map: Local Map 4. Sharpened

Fileemd_47276_additional_17.map
AnnotationLocal Map 4. Sharpened
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Additional map: Local Map 4. Unsharpened

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Additional map: Local Map 4. Half Map 2

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AnnotationLocal Map 4. Half Map 2
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Additional map: Composite Map. Half Map 2

Fileemd_47276_additional_2.map
AnnotationComposite Map. Half Map 2
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Additional map: Local Map 4. Half Map 1

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AnnotationLocal Map 4. Half Map 1
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Additional map: Local Map 5. Half Map 1

Fileemd_47276_additional_21.map
AnnotationLocal Map 5. Half Map 1
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Additional map: Half Map 5. Unsharpened

Fileemd_47276_additional_22.map
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Fileemd_47276_additional_23.map
AnnotationHalf Map 5. Sharpened
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Additional map: Local Map 5. Half Map 2

Fileemd_47276_additional_24.map
AnnotationLocal Map 5. Half Map 2
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Additional map: Composite Map. Sharpened. C2-symmetric

Fileemd_47276_additional_3.map
AnnotationComposite Map. Sharpened. C2-symmetric
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Additional map: Composite Map. Unsharpened. C2-symmetric

Fileemd_47276_additional_4.map
AnnotationComposite Map. Unsharpened. C2-symmetric
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Additional map: Local Map 1. Half Map 2

Fileemd_47276_additional_5.map
AnnotationLocal Map 1. Half Map 2
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Additional map: Local Map 1. Half Map 1

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AnnotationLocal Map 1. Half Map 1
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Additional map: Local Map 2. Half Map 1

Fileemd_47276_additional_7.map
AnnotationLocal Map 2. Half Map 1
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Additional map: Local Map 1. Unsharpened

Fileemd_47276_additional_8.map
AnnotationLocal Map 1. Unsharpened
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Additional map: Local Map 2. Unsharpened

Fileemd_47276_additional_9.map
AnnotationLocal Map 2. Unsharpened
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Half map: Consensus Map. Half Map 1

Fileemd_47276_half_map_1.map
AnnotationConsensus Map. Half Map 1
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Half map: Consensus Map. Half Map 2

Fileemd_47276_half_map_2.map
AnnotationConsensus Map. Half Map 2
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Sample components

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Entire : Human GATOR2 Complex - Apo State

EntireName: Human GATOR2 Complex - Apo State
Components
  • Complex: Human GATOR2 Complex - Apo State
    • Protein or peptide: GATOR2 complex protein MIOS
    • Protein or peptide: GATOR2 complex protein WDR24
    • Protein or peptide: Protein SEC13 homolog

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Supramolecule #1: Human GATOR2 Complex - Apo State

SupramoleculeName: Human GATOR2 Complex - Apo State / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.1 MDa

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Macromolecule #1: GATOR2 complex protein MIOS

MacromoleculeName: GATOR2 complex protein MIOS / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 125.920211 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TKPDILWAPH HVDRFVVCDS ELSLYHVEST VNSELKAGSL RLSEDSAATL LSINSDTPYM KCVAWYLNYD PECLLAVGEA NGRVVLTSL GQDHNSKFKD LIGKEFVPKH ARQCNTLAWN PLDSDWLAAG LDKHRADFSV LIWDICVTKP LYELGQNDAC L SLCWLPRD ...String:
TKPDILWAPH HVDRFVVCDS ELSLYHVEST VNSELKAGSL RLSEDSAATL LSINSDTPYM KCVAWYLNYD PECLLAVGEA NGRVVLTSL GQDHNSKFKD LIGKEFVPKH ARQCNTLAWN PLDSDWLAAG LDKHRADFSV LIWDICVTKP LYELGQNDAC L SLCWLPRD QKLLLAGMHR NLAIFDLRNT SQKMFVNTKA VQGVTVDPYF HDRVASFYEG QVAIWDLRKF EKPVLTLTEQ PK PLTKVAW CPTRTGLLAT LTRDSNIIRL YDMQHTPTPI GDETEPTIIE RSVQPCDNYI ASFAWHPTSQ NRMIVVTPNR TMS DFTVFE RISLAWSPIT SLMWACGRHL YECTEMFVAR SIAADHKDLI HDVSFDFHGR RMATCSSDQS VKVWDKSESG DWHC TASWK THSGSVWRVT WAHPEFGQVL ASCSFDRTAA VWEEIVGESN DKLRGQSHWV KRTTLVDSRT SVTDVKFAPK HMGLM LATC SADGIVRIYE APDVMNLSQW SLQHEISCKL SCSCISWNPS SSRAHSPMIA VGSDDSSPNA MAKVQIFEYN ENTRKY AKA ETLMTVTDPV HDIAFAPNLG RSFHILAIAT KDVRIFTLKP VRKELTSSGG PTKFEIHIVA QFDNHNSQVW RVSWNIT GT VLASSGDDGC VRLWKANYMD NWKCTGILKG NGSPEKDIAT KMRLRALSRY GLDTEQVWRN HILAGNEDPQ LKSLWYTL H FMKQYTEDMD QKSPGNKGSL VYAGIKSIVK SSLGMVESSR HNWSGLDKQS DIQNLNEERI LALQLCGWIK KGTDVDVGP FLNSLVQEGE WERAAAVALF NLDIRRAIQI LNEGASSEKG DLNLNVVAMA LSGYTDEKNS LWREMCSTLR LQLNNPYLCV MFAFLTSET GSYDGVLYEN KVAVRDRVAF ACKFLSDTQL NRYIEKLTNE MKEAGNLEGI LLTGLTKDGV DLMESYVDRT G DVQTASYC MLQGSPLDVL KDERVQYWIE NYRNLLDAWR FWHKRAEFDI HRSKLDPSSK PLAQVFVSCN FCGKSISYKV TS CPGCRKP LPRCALCLIN MGTPVKDKKL AQFNNWFTWC HNCRHGGHAG HMLSWFRDHA ECPVSACTCK CMQLDT

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Macromolecule #2: GATOR2 complex protein WDR24

MacromoleculeName: GATOR2 complex protein WDR24 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102.253469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SVLTGRTMHC HLDAPANAIS VCRDAAQVVV AGRSIFKIYA IEEEQFVEKL NLRVGRKPSL NLSCADVVWH QMDENLLATA ATNGVVVTW NLGRPSRNKQ DQLFTEHKRT VNKVCFHPTE AHVLLSGSQD GFMKCFDLRR KDSVSTFSGQ SESVRDVQFS I RDYFTFAS ...String:
SVLTGRTMHC HLDAPANAIS VCRDAAQVVV AGRSIFKIYA IEEEQFVEKL NLRVGRKPSL NLSCADVVWH QMDENLLATA ATNGVVVTW NLGRPSRNKQ DQLFTEHKRT VNKVCFHPTE AHVLLSGSQD GFMKCFDLRR KDSVSTFSGQ SESVRDVQFS I RDYFTFAS TFENGNVQLW DIRRPDRCER MFTAHNGPVF CCDWHPEDRG WLATGGRDKM VKVWDMTTHR AKEMHCVQTI AS VARVKWR PECRHHLATC SMMVDHNIYV WDVRRPFVPA AMFEEHRDVT TGIAWRHPHD PSFLLSGSKD SSLCQHLFRD ASQ PVERAN PEGLCYGLFG DLAFAAKESL VFAGLASSAL SVFETEPMFV ARSIAADHKD LIHDVSFDFH GRRMATCSSD QSVK VWDKS ESGDWHCTAS WKTHSGSVWR VTWAHPEFGQ VLASCSFDRT AAVWEEIVGQ SHWVKRTTLV DSRTSVTDVK FAPKH MGLM LATCSADGIV RIYEAPDVMN LSQWSLQHEI SCKLSCSCIS WNPSSSRAHS PMIAVGSDDS SPNAMAKVQI FEYNEN TRK YAKAETLMTV TDPVHDIAFA PNLGRSFHIL AIATKDVRIF TLKPVRKELT SSGGPTKFEI HIVAQFDNHN SQVWRVS WN ITGTVLASSG DDGCVRLWKA NYMDNWKCTG ILKGGMRWFV DTAERYALAG RPLAELCDHN AKVARELGRN QVAQTWTM L RIIYCSPFSL LSVSHALYDS RLPPDFFGVL VRDMLHFYAE QGDVQMAVSV LIVLGERVRK DIDEQTQEHW YTSYIDLLQ RFRLWNVSNE VVKLSTSRAV SCLNQASTTL HVNCSHCKRP MSSRGWVCDR CHRCASMCAV CHHVVKGLFV WCQGCSHGGH LQHIMKWLE GSSHCPAGCG HLCEYS

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Macromolecule #3: Protein SEC13 homolog

MacromoleculeName: Protein SEC13 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.445391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ARVTTAYGSY QDANIPFPRT SGARFCGAGY LVYFTRPMTM HRAVSPTEPT PRSLSALSAY HTSKREGSDS GNRQIKAAGK VIIQDGSGS GMVSVINTVD TSHEDMIHDA QMDYYGTRLA TCSSDRSVKI FDVRNGGQIL IADLRGHEGP VWQVAWAHPM Y GNILASCS ...String:
ARVTTAYGSY QDANIPFPRT SGARFCGAGY LVYFTRPMTM HRAVSPTEPT PRSLSALSAY HTSKREGSDS GNRQIKAAGK VIIQDGSGS GMVSVINTVD TSHEDMIHDA QMDYYGTRLA TCSSDRSVKI FDVRNGGQIL IADLRGHEGP VWQVAWAHPM Y GNILASCS YDRKVIIWRE ENGTWEKSHE HAGHDSSVNS VCWAPHDYGL ILACGSSDGA ISLLTYTGEG QWEVKKINNA HT IGCNAVS WAPAVVPDHP SGQKPNYIKR FASGGCDNLI KLWKEEEDGQ WKEEQKLEAH SDWVRDVAWA PSIGLPTSTI ASC SQDGRV FIWTCDDASS NTWSPKLLHK FNDVVWHVSW SITANILAVS GGDNKVTLWK ESVDGQWVCI SDIACLLPVH KSLG ELYIL NVNDIQETCQ KNAASALLVG RKDLVQVWSL ATVATDLCLG PKSDPDLETP WARHPFGRQL LESLLAHYCR LRDVQ TLAM LCSVFEAQSD PRERERDQHD KNKRLLDPAN TQQFDDFKKC YGEILYRWGL REKRAEVLKF VSCPPDPHKG IEFGVY CSH CRSEVRGTQC AICKGFTFQC AICHVAVRGS SNFCLTCGHG GHTSHMMEWF RTQEVCPTGC GCHCLLESTF

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 64.64 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7uhy

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 1148926
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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