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- EMDB-47277: Human GATOR2 complex - Sestrin2 bound state -

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Basic information

Entry
Database: EMDB / ID: EMD-47277
TitleHuman GATOR2 complex - Sestrin2 bound state
Map dataConsensus Map. C2-symmetric
Sample
  • Complex: Human GATOR2 complex bound to Sestrin2
    • Protein or peptide: GATOR2 complex protein MIOS
    • Protein or peptide: Nucleoporin SEH1
    • Protein or peptide: Protein SEC13 homolog
    • Protein or peptide: Sestrin2
  • Protein or peptide: GATOR2 complex protein WDR24
KeywordsSignaling protein / nutrient sensor / mTORC1 pathway / stress-responsive protein
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 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_47277.png

Downloads & links

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Map

FileDownload / File: emd_47277.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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Others
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-0.16606514 - 0.52028763
Average (Standard dev.)0.0015511411 (±0.0143340705)
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_47277_msk_1.map
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Mask #2

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Mask #3

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Mask #4

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Additional map: Composite Map. Sharpened. C2-symmetric

Fileemd_47277_additional_1.map
AnnotationComposite Map. Sharpened. C2-symmetric
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Additional map: Local Map 2. Unsharpened

Fileemd_47277_additional_10.map
AnnotationLocal Map 2. Unsharpened
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Additional map: Local Map 1. Half Map 2

Fileemd_47277_additional_11.map
AnnotationLocal Map 1. Half Map 2
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Additional map: Local Map 1. Half Map 1

Fileemd_47277_additional_12.map
AnnotationLocal Map 1. Half Map 1
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Additional map: Local Map 3. Half Map 2

Fileemd_47277_additional_13.map
AnnotationLocal Map 3. Half Map 2
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Additional map: Local Map 3. Half Map 1

Fileemd_47277_additional_14.map
AnnotationLocal Map 3. Half Map 1
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Additional map: Local Map 3. Sharpened

Fileemd_47277_additional_15.map
AnnotationLocal Map 3. Sharpened
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Additional map: Local Map 3. Unsharpened

Fileemd_47277_additional_16.map
AnnotationLocal Map 3. Unsharpened
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Additional map: Local Map 4. Half Map 2

Fileemd_47277_additional_17.map
AnnotationLocal Map 4. Half Map 2
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Additional map: Local Map 4. Sharpened

Fileemd_47277_additional_18.map
AnnotationLocal Map 4. Sharpened
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Additional map: Local Map 4. Half Map 1

Fileemd_47277_additional_19.map
AnnotationLocal Map 4. Half Map 1
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Additional map: Composite Map. Half Map 1

Fileemd_47277_additional_2.map
AnnotationComposite Map. Half Map 1
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Additional map: Local Map 4. Unsharpened

Fileemd_47277_additional_20.map
AnnotationLocal Map 4. Unsharpened
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Additional map: Composite Map. Half Map 2

Fileemd_47277_additional_3.map
AnnotationComposite Map. Half Map 2
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Additional map: Composite Map. Unsharpened. C2-symmetric

Fileemd_47277_additional_4.map
AnnotationComposite Map. Unsharpened. C2-symmetric
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Additional map: Local Map 2. Unsharpened

Fileemd_47277_additional_5.map
AnnotationLocal Map 2. Unsharpened
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Additional map: Local Map 2. Sharpened

Fileemd_47277_additional_6.map
AnnotationLocal Map 2. Sharpened
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Additional map: Local Map 2. Half Map 2

Fileemd_47277_additional_7.map
AnnotationLocal Map 2. Half Map 2
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Additional map: Local Map 2. Half Map 1

Fileemd_47277_additional_8.map
AnnotationLocal Map 2. Half Map 1
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Additional map: Local Map 1. Sharpened

Fileemd_47277_additional_9.map
AnnotationLocal Map 1. Sharpened
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Half map: Consensus Map. Half Map 1

Fileemd_47277_half_map_1.map
AnnotationConsensus Map. Half Map 1
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Half map: Consensus Map. Half Map 1

Fileemd_47277_half_map_2.map
AnnotationConsensus Map. Half Map 1
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Sample components

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Entire : Human GATOR2 complex bound to Sestrin2

EntireName: Human GATOR2 complex bound to Sestrin2
Components
  • Complex: Human GATOR2 complex bound to Sestrin2
    • Protein or peptide: GATOR2 complex protein MIOS
    • Protein or peptide: Nucleoporin SEH1
    • Protein or peptide: Protein SEC13 homolog
    • Protein or peptide: Sestrin2
  • Protein or peptide: GATOR2 complex protein WDR24

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Supramolecule #1: Human GATOR2 complex bound to Sestrin2

SupramoleculeName: Human GATOR2 complex bound to Sestrin2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.25 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: 126.193492 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 NGSPVEKDIA TKMRLRALSR YGLDTEQVWR NHILAGNEDP QLKSLWYT L HFMKQYTEDM DQKSPGNKGS LVYAGIKSIV KSSLGMVESS RHNWSGLDKQ SDIQNLNEER ILALQLCGWI KKGTDVDVG PFLNSLVQEG EWERAAAVAL FNLDIRRAIQ ILNEGASSEK GDLNLNVVAM ALSGYTDEKN SLWREMCSTL RLQLNNPYLC VMFAFLTSE TGSYDGVLYE NKVAVRDRVA FACKFLSDTQ LNRYIEKLTN EMKEAGNLEG ILLTGLTKDG VDLMESYVDR T GDVQTASY CMLQGSPLDV LKDERVQYWI ENYRNLLDAW RFWHKRAEFD IHRSKLDPSS KPLAQVFVSC NFCGKSISYS KV TSCPGCR KPLPRCALCL INMGTPVSKD KKLAQFNNWF TWCHNCRHGG HAGHMLSWFR DHAECPVSAC TCKCMQLDT

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Macromolecule #2: Nucleoporin SEH1

MacromoleculeName: Nucleoporin SEH1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.601703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ERANPEGLCY GLFGDLAFAA KESLVAEPFA GLASSALSVF ETEPMFVARS IAADHKDLIH DVSFDFHGRR MATCSSDQSV KVWDKSESG DWHCTASWKT HSGSVWRVTW AHPEFGQVLA SCSFDRTAAV WEEIVKLRGQ SHWVKRTTLV DSRTSVTDVK F APKHMGLM ...String:
ERANPEGLCY GLFGDLAFAA KESLVAEPFA GLASSALSVF ETEPMFVARS IAADHKDLIH DVSFDFHGRR MATCSSDQSV KVWDKSESG DWHCTASWKT HSGSVWRVTW AHPEFGQVLA SCSFDRTAAV WEEIVKLRGQ SHWVKRTTLV DSRTSVTDVK F APKHMGLM LATCSADGIV RIYEAPDVMN LSQWSLQHEI SCKLSCSCIS WNPSSSRAHS PMIAVGSDDS SPNAMAKVQI FE YNENTRK YAKAETLMTV TDPVHDIAFA PNLGRSFHIL AIATKDVRIF TLKPVRKELT SSGGPTKFEI HIVAQFDNHN SQV WRVSWN ITGTVLASSG DDGCVRLWKA NYMDNWKCTG ILKGNGGMRW FVDTAERYAL AGRPLAELCD HNAKVARELG RNQV AQTWT MLRIIYCSPD SSSFSLLSVS HALYDSRLPP DFFGVLVRDM LHFYAEQGDV QMAVSVLIVL GERVRKDIDE QTQEH WYTS YIDLLQRFRL WNVSNEVVKL STSRAVSCLN QASTTLHVNC SHCKRPMSSR GWVCDRCHRC ASMCAVCHHV VKGLFV WCQ GCSHGGHLQH IMKWLEGSSH CPAGCGHLCE YS

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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: 62.980754 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ARVTTAYGSY QDANIPFPRT SGARFCGAGY LVYFTRPMTM HRAVSPTEPT PRSLSALSAY HTRWKSKREG SDSGNRQIKA AGKVIIQDG SGSGMVSVIN TVDTSHEDMI HDAQMDYYGT RLATCSSDRS VKIFDVRNGG QILIADLRGH EGPVWQVAWA H PMYGNILA ...String:
ARVTTAYGSY QDANIPFPRT SGARFCGAGY LVYFTRPMTM HRAVSPTEPT PRSLSALSAY HTRWKSKREG SDSGNRQIKA AGKVIIQDG SGSGMVSVIN TVDTSHEDMI HDAQMDYYGT RLATCSSDRS VKIFDVRNGG QILIADLRGH EGPVWQVAWA H PMYGNILA SCSYDRKVII WREENGTWEK SHEHAGHDSS VNSVCWAPHD YGLILACGSS DGAISLLTYT GEGQWEVKKI NN AHTIGCN AVSWAPAVVP GSLIDHPSGQ KPNYIKRFAS GGCDNLIKLW KEEEDGQWKE EQKLEAHSDW VRDVAWAPSI GLP TSTIAS CSQDGRVFIW TCDDASSNTW SPKLLHKFND VVWHVSWSIT ANILAVSGGD NKVTLWKESV DGQWVCISDA CLLP VHKSL GELYILNVND IQETCQKNAA SALLVGRKDL VQVWSLATVA TDLCLGPKSD PDLETPWARH PFGRQLLESL LAHYC RLRD VQTLAMLCSV FEAQSRPQGL PNLTYSDPRE RERDQHDKNK RLLDPANTQQ FDDFKKCYGE ILYRWGLREK RAEVLK FVS C

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Macromolecule #4: Sestrin2

MacromoleculeName: Sestrin2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.005801 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RARRGPRGPS AFIPVEEVLR DNLAVVMGLH PDYFTSFWRL HYLLLHTDGP LASSWRHYIA IMAAARHQCS YLVGSHMAEF LQTGGDPEW LLGLHRAPEK LRKLSEINKL LAHRPWLITK EHIQALLKTG EHTWSLAELI QALVLLTHCH SLSSFVFGCG I LPEHPDML ...String:
RARRGPRGPS AFIPVEEVLR DNLAVVMGLH PDYFTSFWRL HYLLLHTDGP LASSWRHYIA IMAAARHQCS YLVGSHMAEF LQTGGDPEW LLGLHRAPEK LRKLSEINKL LAHRPWLITK EHIQALLKTG EHTWSLAELI QALVLLTHCH SLSSFVFGCG I LPEHPDML CFVEDPTFGY EDFTRRGAQA PPTFRAQDYT WEDHGYSLIQ RLYPEGGQLL DEKFQAAYSL TYNTIAMHSG VD TSVLRRA IWNYIHCVFG IRYDDYDYGE VNQLLERNLK VYIKTVACYP EKTTRRMYNL FWRHFRHSEK VHVNLLLLEA RMQ AALLYA LRAITRYMT

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Macromolecule #5: GATOR2 complex protein WDR24

MacromoleculeName: GATOR2 complex protein WDR24 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.784359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TKPDILWAPH HVDRFVVCDS ELSLYHVEST VNSELKAGSL RLSEDSAATL LSINSDTPYM KCVAWYLNYD PECLLAVGEA NGRVVLTSL GQDHNSKFKD LIGKEFVPKH ARQCNTLAWN PLDSDWLAAG LDKHRADFSV LIWDIPLYEL GQNDACLSLC W LPRDQKLL ...String:
TKPDILWAPH HVDRFVVCDS ELSLYHVEST VNSELKAGSL RLSEDSAATL LSINSDTPYM KCVAWYLNYD PECLLAVGEA NGRVVLTSL GQDHNSKFKD LIGKEFVPKH ARQCNTLAWN PLDSDWLAAG LDKHRADFSV LIWDIPLYEL GQNDACLSLC W LPRDQKLL LAGMHRNLAI FDLRNTSQKM FVNTKAVQGV TVDPYFHDRV ASFYEGQVAI WDLRKFEKPV LTLTEQPKPL TK VAWCPTR TGLLATLTRD SNIIRLYDMQ HTPTPIGDET EPTIIERSVQ PCDNYIASFA WHPTSQNRMI VVTPNRTMSD FTV FSVLTG RTMHCHLDAP ANAISVCRDA AQVVVAGRSI FKIYAIEEEQ FVEKLNLRVG RKPSLNLSCA DVVWHQMDEN LLAT AATNG VVVTWNLGRP SRNKQDQLFT EHKRTVNKVC FHPTEAHVLL SGSQDGFMKC FDLRRKDSVS TFSGQSESVR DVQFS IRDY FTFASTFENG NVQLWDIRRP DRCERMFTAH NGPVFCCDWH PEDRGWLATG GRDKMVKVWD MTTHRAKEMH CVQTIA SVA RVKWRPECRH HLATCSMMVD HNIYVWDVRR PFVPAAMFEE HRDVTTGIAW RHPHDPSFLL SGSKDSSLCQ HLFRDAS QP VPPDPHKGIE FGVYCSHCRS EVRGTQCAIC KGFTFQCAIC HVAVRGSSNF CLTCGHGGHT SHMMEWFRTQ EVCPTGCG C HCLLESTF

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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: 69.44 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: 0.7000000000000001 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: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 605308
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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