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Basic information
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Title | Cryo-EM structure of CASTOR1 bound human GATOR2 complex | |||||||||
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![]() | amino acid sensor / SIGNALING PROTEIN | |||||||||
Function / homology | ![]() oligodendrocyte progenitor proliferation / GATOR2 complex / cellular response to L-arginine / molecular sensor activity / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / central nervous system myelin formation / COPII-coated vesicle cargo loading / nuclear pore outer ring ...oligodendrocyte progenitor proliferation / GATOR2 complex / cellular response to L-arginine / molecular sensor activity / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / central nervous system myelin formation / COPII-coated vesicle cargo loading / nuclear pore outer ring / nuclear pore organization / COPII vesicle coat / Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Amino acids regulate mTORC1 / protein K6-linked ubiquitination / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP independent Mature mRNA / NS1 Mediated Effects on Host Pathways / Transport of the SLBP Dependant Mature mRNA / SUMOylation of SUMOylation proteins / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / 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 / arginine binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / COPII-mediated vesicle transport / vacuolar membrane / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / oligodendrocyte differentiation / SUMOylation of DNA replication proteins / positive regulation of macroautophagy / positive regulation of TOR signaling / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / SUMOylation of DNA damage response and repair proteins / cellular response to nutrient levels / negative regulation of TORC1 signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / signaling adaptor activity / positive regulation of TORC1 signaling / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / MHC class II antigen presentation / cellular response to amino acid starvation / protein sequestering activity / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / HCMV Late Events / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / RHO GTPases Activate Formins / ER to Golgi transport vesicle membrane / RING-type E3 ubiquitin transferase / kinetochore / autophagy / Separation of Sister Chromatids / HCMV Early Events / protein import into nucleus / ubiquitin protein ligase activity / cell junction / nuclear envelope / protein transport / snRNP Assembly / regulation of autophagy / defense response to Gram-positive bacterium / lysosomal membrane / cell division / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.59 Å | |||||||||
![]() | Su M-Y | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Cryo-EM structures of amino acid sensors bound to the human GATOR2 complex. Authors: Ming-Yuan Su / Fei Teng / Shan Wang / Xinyi Mai / Huan Zeng / Juan Li / Xiaoxiao Song / Xi Wang / Goran Stjepanovic / ![]() Abstract: Mammalian cells regulate growth by integrating environmental cues through the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway. The human GATOR2 complex, comprising WDR59, WDR24, ...Mammalian cells regulate growth by integrating environmental cues through the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway. The human GATOR2 complex, comprising WDR59, WDR24, Mios, Sec13, and Seh1l, is key to mTORC1 regulation. Under amino acid deprivation, GATOR2 is inhibited through interactions with cytosolic leucine sensor Sestrin2 and arginine sensor cytosolic arginine sensor for mTORC1 subunit 1 (CASTOR1). Amino acid abundance relieves this inhibition, allowing GATOR2 to antagonize the repressor GATOR1. Despite its importance, GATOR2's inhibition mechanisms were unclear. Here, we present cryo-electron microscopy (cryo-EM) structures of GATOR2 in three inhibitory states: CASTOR1 bound, Sestrin2 bound, and dual bound. CASTOR1 engages the Mios WD40 β-propellers, while Sestrin2 interacts with the WDR24-Seh1l subcomplex, inducing conformational movements. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) reveals dynamic motions in apo-GATOR2 and its complexes with amino acid sensors, as well as the effects of amino acid supplementation. These findings unravel the interactions between GATOR2 and amino acid sensors, providing a perspective on the regulation of the mTORC1 pathway by nutrient-sensing machinery. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 366.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 43.8 KB 43.8 KB | Display Display | ![]() |
Images | ![]() | 47.2 KB | ||
Masks | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 744.3 MB 744.3 MB 744.3 MB 744.3 MB 744.3 MB 744.3 MB 744.3 MB | ![]() | |
Filedesc metadata | ![]() | 8.9 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 656.4 MB 369.2 MB 2 MB 369.6 MB 369.9 MB 368 MB 369.3 MB 371.1 MB 368.6 MB 369.6 MB 689.9 MB 689.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 984.8 KB | Display | ![]() |
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Full document | ![]() | 984.4 KB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 23.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9lvkMC ![]() 9lvjC ![]() 9lwfC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Cryo-EM structure of CASTOR1 bound human GATOR2 complex
Entire | Name: Cryo-EM structure of CASTOR1 bound human GATOR2 complex |
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Components |
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-Supramolecule #1: Cryo-EM structure of CASTOR1 bound human GATOR2 complex
Supramolecule | Name: Cryo-EM structure of CASTOR1 bound human GATOR2 complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: GATOR2 complex protein MIOS
Macromolecule | Name: GATOR2 complex protein MIOS / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 98.700391 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSGTKPDILW APHHVDRFVV CDSELSLYHV ESTVNSELKA GSLRLSEDSA ATLLSINSDT PYMKCVAWYL NYDPECLLAV GQANGRVVL TSLGQDHNSK FKDLIGKEFV PKHARQCNTL AWNPLDSNWL AAGLDKHRAD FSVLIWDICS KYTPDIVPME K VKLSAGET ...String: MSGTKPDILW APHHVDRFVV CDSELSLYHV ESTVNSELKA GSLRLSEDSA ATLLSINSDT PYMKCVAWYL NYDPECLLAV GQANGRVVL TSLGQDHNSK FKDLIGKEFV PKHARQCNTL AWNPLDSNWL AAGLDKHRAD FSVLIWDICS KYTPDIVPME K VKLSAGET ETTLLVTKPL YELGQNDACL SLCWLPRDQK LLLAGMHRNL AIFDLRNTSQ KMFVNTKAVQ GVTVDPYFHD RV ASFYEGQ VAIWDLRKFE KPVLTLTEQP KPLTKVAWCP TRTGLLATLT RDSNIIRLYD MQHTPTPIGD ETEPTIIERS VQP CDNYIA SFAWHPTSQN RMIVVTPNRT MSDFTVFERI SLAWSPITSL MWACGRHLYE CTEEENDNSL EKDIATKMRL RALS RYGLD TEQVWRNHIL AGNEDPQLKS LWYTLHFMKQ YTEDMDQKSP GNKGSLVYAG IKSIVKSSLG MVESSRHNWS GLDKQ SDIQ NLNEERILAL QLCGWIKKGT DVDVGPFLNS LVQEGEWERA AAVALFNLDI RRAIQILNEG ASSEKGDLNL NVVAMA LSG YTDEKNSLWR EMCSTLRLQL NNPYLCVMFA FLTSETGSYD GVLYENKVAV RDRVAFACKF LSDTQLNRYI EKLTNEM KE AGNLEGILLT GLTKDGVDLM ESYVDRTGDV QTASYCMLQG SPLDVLKDER VQYWIENYRN LLDAWRFWHK RAEFDIHR S KLDPSSKPLA QVFVSCNFCG KSISYSCSAV PHQGRGFSQY GVSGSPTKSK VTSCPGCRKP LPRCALCLIN MGTPVSSCP GGTKSDEKVD LSKDKKLAQF NNWFTWCHNC RHGGHAGHML SWFRDHAECP VSACTCKCMQ LDTTGNLVPA ETVQP UniProtKB: GATOR2 complex protein MIOS |
-Macromolecule #2: GATOR2 complex protein WDR24
Macromolecule | Name: GATOR2 complex protein WDR24 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 88.326953 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MEKMSRVTTA LGGSVLTGRT MHCHLDAPAN AISVCRDAAQ VVVAGRSIFK IYAIEEEQFV EKLNLRVGRK PSLNLSCADV VWHQMDENL LATAATNGVV VTWNLGRPSR NKQDQLFTEH KRTVNKVCFH PTEAHVLLSG SQDGFMKCFD LRRKDSVSTF S GQSESVRD ...String: MEKMSRVTTA LGGSVLTGRT MHCHLDAPAN AISVCRDAAQ VVVAGRSIFK IYAIEEEQFV EKLNLRVGRK PSLNLSCADV VWHQMDENL LATAATNGVV VTWNLGRPSR NKQDQLFTEH KRTVNKVCFH PTEAHVLLSG SQDGFMKCFD LRRKDSVSTF S GQSESVRD VQFSIRDYFT FASTFENGNV QLWDIRRPDR CERMFTAHNG PVFCCDWHPE DRGWLATGGR DKMVKVWDMT TH RAKEMHC VQTIASVARV KWRPECRHHL ATCSMMVDHN IYVWDVRRPF VPAAMFEEHR DVTTGIAWRH PHDPSFLLSG SKD SSLCQH LFRDASQPVE RANPEGLCYG LFGDLAFAAK ESLVAAESGR KPYTGDRRHP IFFKRKLDPA EPFAGLASSA LSVF ETEPG GGGMRWFVDT AERYALAGRP LAELCDHNAK VARELGRNQV AQTWTMLRII YCSPGLVPTA NLNHSVGKGG SCGLP LMNS FNLKDMAPGL GSETRLDRSK GDARSDTVLL DSSATLITNE DNEETEGSDV PADYLLGDVE GEEDELYLLD PEHAHP EDP ECVLPQEAFP LRHEIVDTPP GPEHLQDKAD SPHVSGSEAD VASLAPVDSS FSLLSVSHAL YDSRLPPDFF GVLVRDM LH FYAEQGDVQM AVSVLIVLGE RVRKDIDEQT QEHWYTSYID LLQRFRLWNV SNEVVKLSTS RAVSCLNQAS TTLHVNCS H CKRPMSSRGW VCDRCHRCAS MCAVCHHVVK GLFVWCQGCS HGGHLQHIMK WLEGSSHCPA GCGHLCEYS UniProtKB: GATOR2 complex protein WDR24 |
-Macromolecule #3: GATOR2 complex protein WDR59
Macromolecule | Name: GATOR2 complex protein WDR59 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 109.938391 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MAARWSSENV VVEFRDSQAT AMSVDCLGQH AVLSGRRFLY IVNLDAPFEG HRKISRQSKW DIGAVQWNPH DSFAHYFAAS SNQRVDLYK WKDGSGEVGT TLQGHTRVIS DLDWAVFEPD LLVTSSVDTY IYIWDIKDTR KPTVALSAVA GASQVKWNKK N ANCLATSH ...String: MAARWSSENV VVEFRDSQAT AMSVDCLGQH AVLSGRRFLY IVNLDAPFEG HRKISRQSKW DIGAVQWNPH DSFAHYFAAS SNQRVDLYK WKDGSGEVGT TLQGHTRVIS DLDWAVFEPD LLVTSSVDTY IYIWDIKDTR KPTVALSAVA GASQVKWNKK N ANCLATSH DGDVRIWDKR KPSTAVEYLA AHLSKIHGLD WHPDSEHILA TSSQDNSVKF WDYRQPRKYL NILPCQVPVW KA RYTPFSN GLVTVMVPQL RRENSLLLWN VFDLNTPVHT FVGHDDVVLE FQWRKQKEGS KDYQLVTWSR DQTLRMWRVD SQM QRLCAN DILDGVDEFI ESISLLPEPE KTLHTEDTDH QHTASHGEEE ALKEDPPRNL LEERKSDQLG LPQTLQQEFS LINV QIRNV NVEMDAADRS CTVSVHCSNH RVKMLVKFPA QYPNNAAPSF QFINPTTITS TMKAKLLKIL KDTALQKVKR GQSCL EPCL RQLVSCLESF VNQEDSASSN PFALPNSVTP PLPTFARVTT AYGSYQDANI PFPRTSGARF CGAGYLVYFT RPMTMH RAV SPTEPTPRSL SALSAYHTGL IAPMKIRTEA PGNLRLYSGS PTRSEKEQVS ISSFYYKERK SRRWKSKREG SDSGNRQ IK AAGKVIIQDI ACLLPVHKSL GELYILNVND IQETCQKNAA SALLVGRKDL VQVWSLATVA TDLCLGPKSD PDLETPWA R HPFGRQLLES LLAHYCRLRD VQTLAMLCSV FEAQSRPQGL PNPFGPFPNR SSNLVVSHSR YPSFTSSGSC SSMSDPGLN TGGWNIAGRE AEHLSSPWGE SSPEELRFGS LTYSDPRERE RDQHDKNKRL LDPANTQQFD DFKKCYGEIL YRWGLREKRA EVLKFVSCP PDPHKGIEFG VYCSHCRSEV RGTQCAICKG FTFQCAICHV AVRGSSNFCL TCGHGGHTSH MMEWFRTQEV C PTGCGCHC LLESTF UniProtKB: GATOR2 complex protein WDR59 |
-Macromolecule #4: Isoform B of Nucleoporin SEH1
Macromolecule | Name: Isoform B of Nucleoporin SEH1 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 46.636289 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MFVARSIAAD HKDLIHDVSF DFHGRRMATC SSDQSVKVWD KSESGDWHCT ASWKTHSGSV WRVTWAHPEF GQVLASCSFD RTAAVWEEI VGESNDKLRG QSHWVKRTTL VDSRTSVTDV KFAPKHMGLM LATCSADGIV RIYEAPDVMN LSQWSLQHEI S CKLSCSCI ...String: MFVARSIAAD HKDLIHDVSF DFHGRRMATC SSDQSVKVWD KSESGDWHCT ASWKTHSGSV WRVTWAHPEF GQVLASCSFD RTAAVWEEI VGESNDKLRG QSHWVKRTTL VDSRTSVTDV KFAPKHMGLM LATCSADGIV RIYEAPDVMN LSQWSLQHEI S CKLSCSCI SWNPSSSRAH SPMIAVGSDD SSPNAMAKVQ IFEYNENTRK YAKAETLMTV TDPVHDIAFA PNLGRSFHIL AI ATKDVRI FTLKPVRKEL TSSGGPTKFE IHIVAQFDNH NSQVWRVSWN ITGTVLASSG DDGCVRLWKA NYMDNWKCTG ILK GNGSPV NGSSQQGTSN PSLGSTIPSL QNSLNGSSAG RYFFTPLDSP RAGSRWSSYA QLLPPPPPPL VEHSCDADTA NLQY PHPRR RYLSRPLNPL PENEGI UniProtKB: Nucleoporin SEH1 |
-Macromolecule #5: Isoform 3 of Protein SEC13 homolog
Macromolecule | Name: Isoform 3 of Protein SEC13 homolog / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40.791668 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MREPVLTWCV PLELLCSHPL PLSAFLKSQV KLYTYRACAG KDEMGKMVSV INTVDTSHED MIHDAQMDYY GTRLATCSSD RSVKIFDVR NGGQILIADL RGHEGPVWQV AWAHPMYGNI LASCSYDRKV IIWREENGTW EKSHEHAGHD SSVNSVCWAP H DYGLILAC ...String: MREPVLTWCV PLELLCSHPL PLSAFLKSQV KLYTYRACAG KDEMGKMVSV INTVDTSHED MIHDAQMDYY GTRLATCSSD RSVKIFDVR NGGQILIADL RGHEGPVWQV AWAHPMYGNI LASCSYDRKV IIWREENGTW EKSHEHAGHD SSVNSVCWAP H DYGLILAC GSSDGAISLL TYTGEGQWEV KKINNAHTIG CNAVSWAPAV VPGSLIDHPS GQKPNYIKRF ASGGCDNLIK LW KEEEDGQ WKEEQKLEAH SDWVRDVAWA PSIGLPTSTI ASCSQDGRVF IWTCDDASSN TWSPKLLHKF NDVVWHVSWS ITA NILAVS GGDNKVTLWK ESVDGQWVCI SDVNKGQGSV SASVTEGQQN EQ UniProtKB: Protein SEC13 homolog |
-Macromolecule #6: Cytosolic arginine sensor for mTORC1 subunit 1
Macromolecule | Name: Cytosolic arginine sensor for mTORC1 subunit 1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 36.265234 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MELHILEHRV RVLSVARPGL WLYTHPLIKL LFLPRRSRCK FFSLTETPED YTLMVDEEGF KELPPSEFLQ VAEATWLVLN VSSHSGAAV QAAGVTKIAR SVIAPLAEHH VSVLMLSTYQ TDFILVREQD LSVVIHTLAQ EFDIYREVGG EPVPVTRDDS S NGFPRTQH ...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 ISTFNFAHAL VPEDGIGSVI EVL QRRQEG LAS UniProtKB: Cytosolic arginine sensor for mTORC1 subunit 1 |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 31 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.52 e/Å2 Details: The total dose on the specimen was 51.52, 51.87, 49,72, 46.79, 47.65, 48.04 and 48.04 e-/A2 fractionated over 50 frames |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |