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- EMDB-26857: cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex with s... -

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Basic information

Entry
Database: EMDB / ID: EMD-26857
Titlecryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex with symmetry expansion
Map data
Sample
  • Complex: The mTORC1-TFEB-Rag-Ragulator complex
    • Protein or peptide: x 11 types
  • Ligand: x 4 types
KeywordsmTORC1 / TFEB / Lysosome biogenesis / Autophagy / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / regulation of cholesterol efflux / Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / Ragulator complex / cardiac cell development / positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / RNA polymerase III type 2 promoter sequence-specific DNA binding ...regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / regulation of cholesterol efflux / Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / Ragulator complex / cardiac cell development / positive regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / regulation of TORC1 signaling / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / positive regulation of odontoblast differentiation / antibacterial innate immune response / regulation of lysosome organization / TORC1 complex / protein localization to lysosome / negative regulation of lysosome organization / regulation of osteoclast differentiation / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / lysosome localization / embryonic placenta development / MTOR signalling / cellular response to L-leucine / Energy dependent regulation of mTOR by LKB1-AMPK / cellular response to nutrient / regulation of autophagosome assembly / Amino acids regulate mTORC1 / endosome organization / Dengue virus modulates apoptosis / cellular response to methionine / positive regulation of osteoclast differentiation / TORC2 signaling / cellular response to osmotic stress / TORC1 signaling / anoikis / kinase activator activity / protein localization to membrane / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / inositol hexakisphosphate binding / negative regulation of protein localization to nucleus / positive regulation of ubiquitin-dependent protein catabolic process / lysosome organization / azurophil granule membrane / endosomal transport / regulation of cell size / negative regulation of macroautophagy / regulation of TOR signaling / humoral immune response / Macroautophagy / small GTPase-mediated signal transduction / RHOJ GTPase cycle / Constitutive Signaling by AKT1 E17K in Cancer / RHOQ GTPase cycle / behavioral response to pain / positive regulation of transcription by RNA polymerase III / positive regulation of protein kinase activity / regulation of receptor recycling / CDC42 GTPase cycle / response to amino acid / social behavior / tertiary granule membrane / neuronal action potential / TOR signaling / RHOG GTPase cycle / RHOH GTPase cycle / mTORC1-mediated signalling / ficolin-1-rich granule membrane / RAC3 GTPase cycle / HSF1-dependent transactivation / RAC2 GTPase cycle / CD28 dependent PI3K/Akt signaling / positive regulation of TOR signaling / positive regulation of translational initiation / positive regulation of lipid biosynthetic process / protein serine/threonine kinase inhibitor activity / enzyme-substrate adaptor activity / protein kinase activator activity / positive regulation of epithelial to mesenchymal transition / T cell costimulation / vascular endothelial cell response to laminar fluid shear stress / specific granule membrane / positive regulation of G1/S transition of mitotic cell cycle / cellular response to nutrient levels / regulation of cellular response to heat / 'de novo' pyrimidine nucleobase biosynthetic process / regulation of macroautophagy / cytoskeleton organization / positive regulation of endothelial cell proliferation / negative regulation of insulin receptor signaling pathway
Similarity search - Function
Transcription factor EB / MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR5 ...Transcription factor EB / MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / RagA/B / RagC/D / Gtr1/RagA G protein / Gtr1/RagA G protein conserved region / Raptor, N-terminal CASPase-like domain / Ragulator complex protein LAMTOR2-like / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / Target of rapamycin complex subunit LST8 / HEAT repeat / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / HEAT repeat / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / : / Serine/threonine-protein kinase ATR-like, HEAT repeats / Helix-loop-helix DNA-binding domain / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / Armadillo-type fold / 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 / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ragulator complex protein LAMTOR5 / Transcription factor EB / Serine/threonine-protein kinase mTOR / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR1 / Ras-related GTP-binding protein A / Regulatory-associated protein of mTOR / Target of rapamycin complex subunit LST8 / Ras-related GTP-binding protein C / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCui Z / Hurley J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111730 United States
CitationJournal: Nature / Year: 2023
Title: Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex.
Authors: Zhicheng Cui / Gennaro Napolitano / Mariana E G de Araujo / Alessandra Esposito / Jlenia Monfregola / Lukas A Huber / Andrea Ballabio / James H Hurley /
Abstract: The transcription factor TFEB is a master regulator of lysosomal biogenesis and autophagy. The phosphorylation of TFEB by the mechanistic target of rapamycin complex 1 (mTORC1) is unique in its ...The transcription factor TFEB is a master regulator of lysosomal biogenesis and autophagy. The phosphorylation of TFEB by the mechanistic target of rapamycin complex 1 (mTORC1) is unique in its mTORC1 substrate recruitment mechanism, which is strictly dependent on the amino acid-mediated activation of the RagC GTPase activating protein FLCN. TFEB lacks the TOR signalling motif responsible for the recruitment of other mTORC1 substrates. We used cryogenic-electron microscopy to determine the structure of TFEB as presented to mTORC1 for phosphorylation, which we refer to as the 'megacomplex'. Two full Rag-Ragulator complexes present each molecule of TFEB to the mTOR active site. One Rag-Ragulator complex is bound to Raptor in the canonical mode seen previously in the absence of TFEB. A second Rag-Ragulator complex (non-canonical) docks onto the first through a RagC GDP-dependent contact with the second Ragulator complex. The non-canonical Rag dimer binds the first helix of TFEB with a RagC-dependent aspartate clamp in the cleft between the Rag G domains. In cellulo mutation of the clamp drives TFEB constitutively into the nucleus while having no effect on mTORC1 localization. The remainder of the 108-amino acid TFEB docking domain winds around Raptor and then back to RagA. The double use of RagC GDP contacts in both Rag dimers explains the strong dependence of TFEB phosphorylation on FLCN and the RagC GDP state.
History
DepositionMay 5, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26857.png

Downloads & links

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Map

FileDownload / File: emd_26857.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 588 pix.
= 617.4 Å		1.05 Å/pix.
x 588 pix.
= 617.4 Å		1.05 Å/pix.
x 588 pix.
= 617.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.7518466 - 2.984613
Average (Standard dev.)0.0012576251 (±0.029955782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions588588588
Spacing588588588
CellA=B=C: 617.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_26857_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26857_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : The mTORC1-TFEB-Rag-Ragulator complex

EntireName: The mTORC1-TFEB-Rag-Ragulator complex
Components
  • Complex: The mTORC1-TFEB-Rag-Ragulator complex
    • Protein or peptide: Serine/threonine-protein kinase mTOR
    • Protein or peptide: Target of rapamycin complex subunit LST8
    • Protein or peptide: Regulatory-associated protein of mTOR
    • Protein or peptide: Ras-related GTP-binding protein A
    • Protein or peptide: Ras-related GTP-binding protein C
    • Protein or peptide: Ragulator complex protein LAMTOR1
    • Protein or peptide: Ragulator complex protein LAMTOR2
    • Protein or peptide: Ragulator complex protein LAMTOR3
    • Protein or peptide: Ragulator complex protein LAMTOR4
    • Protein or peptide: Ragulator complex protein LAMTOR5
    • Protein or peptide: Transcription factor EB
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: The mTORC1-TFEB-Rag-Ragulator complex

SupramoleculeName: The mTORC1-TFEB-Rag-Ragulator complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11

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Macromolecule #1: Serine/threonine-protein kinase mTOR

MacromoleculeName: Serine/threonine-protein kinase mTOR / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 289.257969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLGTGPAAAT TAATTSSNVS VLQQFASGLK SRNEETRAKA AKELQHYVTM ELREMSQEES TRFYDQLNHH IFELVSSSDA NERKGGILA IASLIGVEGG NATRIGRFAN YLRNLLPSND PVVMEMASKA IGRLAMAGDT FTAEYVEFEV KRALEWLGAD R NEGRRHAA ...String:
MLGTGPAAAT TAATTSSNVS VLQQFASGLK SRNEETRAKA AKELQHYVTM ELREMSQEES TRFYDQLNHH IFELVSSSDA NERKGGILA IASLIGVEGG NATRIGRFAN YLRNLLPSND PVVMEMASKA IGRLAMAGDT FTAEYVEFEV KRALEWLGAD R NEGRRHAA VLVLRELAIS VPTFFFQQVQ PFFDNIFVAV WDPKQAIREG AVAALRACLI LTTQREPKEM QKPQWYRHTF EE AEKGFDE TLAKEKGMNR DDRIHGALLI LNELVRISSM EGERLREEME EITQQQLVHD KYCKDLMGFG TKPRHITPFT SFQ AVQPQQ SNALVGLLGY SSHQGLMGFG TSPSPAKSTL VESRCCRDLM EEKFDQVCQW VLKCRNSKNS LIQMTILNLL PRLA AFRPS AFTDTQYLQD TMNHVLSCVK KEKERTAAFQ ALGLLSVAVR SEFKVYLPRV LDIIRAALPP KDFAHKRQKA MQVDA TVFT CISMLARAMG PGIQQDIKEL LEPMLAVGLS PALTAVLYDL SRQIPQLKKD IQDGLLKMLS LVLMHKPLRH PGMPKG LAH QLASPGLTTL PEASDVGSIT LALRTLGSFE FEGHSLTQFV RHCADHFLNS EHKEIRMEAA RTCSRLLTPS IHLISGH AH VVSQTAVQVV ADVLSKLLVV GITDPDPDIR YCVLASLDER FDAHLAQAEN LQALFVALND QVFEIRELAI CTVGRLSS M NPAFVMPFLR KMLIQILTEL EHSGIGRIKE QSARMLGHLV SNAPRLIRPY MEPILKALIL KLKDPDPDPN PGVINNVLA TIGELAQVSG LEMRKWVDEL FIIIMDMLQD SSLLAKRQVA LWTLGQLVAS TGYVVEPYRK YPTLLEVLLN FLKTEQNQGT RREAIRVLG LLGALDPYKH KVNIGMIDQS RDASAVSLSE SKSSQDSSDY STSEMLVNMG NLPLDEFYPA VSMVALMRIF R DQSLSHHH TMVVQAITFI FKSLGLKCVQ FLPQVMPTFL NVIRVCDGAI REFLFQQLGM LVSFVKSHIR PYMDEIVTLM RE FWVMNTS IQSTIILLIE QIVVALGGEF KLYLPQLIPH MLRVFMHDNS PGRIVSIKLL AAIQLFGANL DDYLHLLLPP IVK LFDAPE APLPSRKAAL ETVDRLTESL DFTDYASRII HPIVRTLDQS PELRSTAMDT LSSLVFQLGK KYQIFIPMVN KVLV RHRIN HQRYDVLICR IVKGYTLADE EEDPLIYQHR MLRSGQGDAL ASGPVETGPM KKLHVSTINL QKAWGAARRV SKDDW LEWL RRLSLELLKD SSSPSLRSCW ALAQAYNPMA RDLFNAAFVS CWSELNEDQQ DELIRSIELA LTSQDIAEVT QTLLNL AEF MEHSDKGPLP LRDDNGIVLL GERAAKCRAY AKALHYKELE FQKGPTPAIL ESLISINNKL QQPEAAAGVL EYAMKHF GE LEIQATWYEK LHEWEDALVA YDKKMDTNKD DPELMLGRMR CLEALGEWGQ LHQQCCEKWT LVNDETQAKM ARMAAAAA W GLGQWDSMEE YTCMIPRDTH DGAFYRAVLA LHQDLFSLAQ QCIDKARDLL DAELTAMAGE SYSRAYGAMV SCHMLSELE EVIQYKLVPE RREIIRQIWW ERLQGCQRIV EDWQKILMVR SLVVSPHEDM RTWLKYASLC GKSGRLALAH KTLVLLLGVD PSRQLDHPL PTVHPQVTYA YMKNMWKSAR KIDAFQHMQH FVQTMQQQAQ HAIATEDQQH KQELHKLMAR CFLKLGEWQL N LQGINEST IPKVLQYYSA ATEHDRSWYK AWHAWAVMNF EAVLHYKHQN QARDEKKKLR HASGANITNA TTAATTAATA TT TASTEGS NSESEAESTE NSPTPSPLQK KVTEDLSKTL LMYTVPAVQG FFRSISLSRG NNLQDTLRVL TLWFDYGHWP DVN EALVEG VKAIQIDTWL QVIPQLIARI DTPRPLVGRL IHQLLTDIGR YHPQALIYPL TVASKSTTTA RHNAANKILK NMCE HSNTL VQQAMMVSEE LIRVAILWHE MWHEGLEEAS RLYFGERNVK GMFEVLEPLH AMMERGPQTL KETSFNQAYG RDLME AQEW CRKYMKSGNV KDLTQAWDLY YHVFRRISKQ LPQLTSLELQ YVSPKLLMCR DLELAVPGTY DPNQPIIRIQ SIAPSL QVI TSKQRPRKLT LMGSNGHEFV FLLKGHEDLR QDERVMQLFG LVNTLLANDP TSLRKNLSIQ RYAVIPLSTN SGLIGWV PH CDTLHALIRD YREKKKILLN IEHRIMLRMA PDYDHLTLMQ KVEVFEHAVN NTAGDDLAKL LWLKSPSSEV WFDRRTNY T RSLAVMSMVG YILGLGDRHP SNLMLDRLSG KILHIDFGDC FEVAMTREKF PEKIPFRLTR MLTNAMEVTG LDGNYRITC HTVMEVLREH KDSVMAVLEA FVYDPLLNWR LMDTNTKGNK RSRTRTDSYS AGQSVEILDG VELGEPAHKK TGTTVPESIH SFIGDGLVK PEALNKKAIQ IINRVRDKLT GRDFSHDDTL DVPTQVELLI KQATSHENLC QCYIGWCPFW

UniProtKB: Serine/threonine-protein kinase mTOR

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Macromolecule #2: Target of rapamycin complex subunit LST8

MacromoleculeName: Target of rapamycin complex subunit LST8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.91009 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNTSPGTVGS DPVILATAGY DHTVRFWQAH SGICTRTVQH QDSQVNALEV TPDRSMIAAA GYQHIRMYDL NSNNPNPIIS YDGVNKNIA SVGFHEDGRW MYTGGEDCTA RIWDLRSRNL QCQRIFQVNA PINCVCLHPN QAELIVGDQS GAIHIWDLKT D HNEQLIPE ...String:
MNTSPGTVGS DPVILATAGY DHTVRFWQAH SGICTRTVQH QDSQVNALEV TPDRSMIAAA GYQHIRMYDL NSNNPNPIIS YDGVNKNIA SVGFHEDGRW MYTGGEDCTA RIWDLRSRNL QCQRIFQVNA PINCVCLHPN QAELIVGDQS GAIHIWDLKT D HNEQLIPE PEVSITSAHI DPDASYMAAV NSTGNCYVWN LTGGIGDEVT QLIPKTKIPA HTRYALQCRF SPDSTLLATC SA DQTCKIW RTSNFSLMTE LSIKSGNPGE SSRGWMWGCA FSGDSQYIVT ASSDNLARLW CVETGEIKRE YGGHQKAVVC LAF NDSVLG

UniProtKB: Target of rapamycin complex subunit LST8

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Macromolecule #3: Regulatory-associated protein of mTOR

MacromoleculeName: Regulatory-associated protein of mTOR / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 149.200016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MESEMLQSPL LGLGEEDEAD LTDWNLPLAF MKKRHCEKIE GSKSLAQSWR MKDRMKTVSV ALVLCLNVGV DPPDVVKTTP CARLECWID PLSMGPQKAL ETIGANLQKQ YENWQPRARY KQSLDPTVDE VKKLCTSLRR NAKEERVLFH YNGHGVPRPT V NGEVWVFN ...String:
MESEMLQSPL LGLGEEDEAD LTDWNLPLAF MKKRHCEKIE GSKSLAQSWR MKDRMKTVSV ALVLCLNVGV DPPDVVKTTP CARLECWID PLSMGPQKAL ETIGANLQKQ YENWQPRARY KQSLDPTVDE VKKLCTSLRR NAKEERVLFH YNGHGVPRPT V NGEVWVFN KNYTQYIPLS IYDLQTWMGS PSIFVYDCSN AGLIVKSFKQ FALQREQELE VAAINPNHPL AQMPLPPSMK NC IQLAACE ATELLPMIPD LPADLFTSCL TTPIKIALRW FCMQKCVSLV PGVTLDLIEK IPGRLNDRRT PLGELNWIFT AIT DTIAWN VLPRDLFQKL FRQDLLVASL FRNFLLAERI MRSYNCTPVS SPRLPPTYMH AMWQAWDLAV DICLSQLPTI IEEG TAFRH SPFFAEQLTA FQVWLTMGVE NRNPPEQLPI VLQVLLSQVH RLRALDLLGR FLDLGPWAVS LALSVGIFPY VLKLL QSSA RELRPLLVFI WAKILAVDSS CQADLVKDNG HKYFLSVLAD PYMPAEHRTM TAFILAVIVN SYHTGQEACL QGNLIA ICL EQLNDPHPLL RQWVAICLGR IWQNFDSARW CGVRDSAHEK LYSLLSDPIP EVRCAAVFAL GTFVGNSAER TDHSTTI DH NVAMMLAQLV SDGSPMVRKE LVVALSHLVV QYESNFCTVA LQFIEEEKNY ALPSPATTEG GSLTPVRDSP CTPRLRSV S SYGNIRAVAT ARSLNKSLQN LSLTEESGGA VAFSPGNLST SSSASSTLGS PENEEHILSF ETIDKMRRAS SYSSLNSLI GVSFNSVYTQ IWRVLLHLAA DPYPEVSDVA MKVLNSIAYK ATVNARPQRV LDTSSLTQSA PASPTNKGVH IHQAGGSPPA SSTSSSSLT NDVAKQPVSR DLPSGRPGTT GPAGAQYTPH SHQFPRTRKM FDKGPEQTAD DADDAAGHKS FISATVQTGF C DWSARYFA QPVMKIPEEH DLESQIRKER EWRFLRNSRV RRQAQQVIQK GITRLDDQIF LNRNPGVPSV VKFHPFTPCI AV ADKDSIC FWDWEKGEKL DYFHNGNPRY TRVTAMEYLN GQDCSLLLTA TDDGAIRVWK NFADLEKNPE MVTAWQGLSD MLP TTRGAG MVVDWEQETG LLMSSGDVRI VRIWDTDREM KVQDIPTGAD SCVTSLSCDS HRSLIVAGLG DGSIRVYDRR MALS ECRVM TYREHTAWVV KASLQKRPDG HIVSVSVNGD VRIFDPRMPE SVNVLQIVKG LTALDIHPQA DLIACGSVNQ FTAIY NSSG ELINNIKYYD GFMGQRVGAI SCLAFHPHWP HLAVGSNDYY ISVYSVEKRV R

UniProtKB: Regulatory-associated protein of mTOR

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Macromolecule #4: Ras-related GTP-binding protein A

MacromoleculeName: Ras-related GTP-binding protein A / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.600195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPNTAMKKKV LLMGKSGSGK TSMRSIIFAN YIARDTRRLG ATIDVEHSHV RFLGNLVLNL WDCGGLDTFM ENYFTSQRDN IFRNVEVLI YVFDVESREL EKDMHYYQSC LEAILQNSPD AKIFCLVHKM DLVQEDQRDL IFKEREEDLR RLSRPLECAC F RTSIWDET ...String:
MPNTAMKKKV LLMGKSGSGK TSMRSIIFAN YIARDTRRLG ATIDVEHSHV RFLGNLVLNL WDCGGLDTFM ENYFTSQRDN IFRNVEVLI YVFDVESREL EKDMHYYQSC LEAILQNSPD AKIFCLVHKM DLVQEDQRDL IFKEREEDLR RLSRPLECAC F RTSIWDET LYKAWSSIVY QLIPNVQQLE MNLRNFAQII EADEVLLFER ATFLVISHYQ CKEQRDVHRF EKISNIIKQF KL SCSKLAA SFQSMEVRNS NFAAFIDIFT SNTYVMVVMS DPSIPSAATL INIRNARKHF EKLERVDGPK HSLLMR

UniProtKB: Ras-related GTP-binding protein A

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Macromolecule #5: Ras-related GTP-binding protein C

MacromoleculeName: Ras-related GTP-binding protein C / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.298859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLQYGAEET PLAGSYGAAD SFPKDFGYGV EEEEEEAAAA GGGVGAGAGG GCGPGGADSS KPRILLMGLR RSGKNSIQKV VFHKMSPNE TLFLESTNKI YKDDISNSSF VNFQIWDFPG QMDFFDPTFD YEMIFRGTGA LIYVIDAQDD YMEALTRLHI T VSKAYKVN ...String:
MSLQYGAEET PLAGSYGAAD SFPKDFGYGV EEEEEEAAAA GGGVGAGAGG GCGPGGADSS KPRILLMGLR RSGKNSIQKV VFHKMSPNE TLFLESTNKI YKDDISNSSF VNFQIWDFPG QMDFFDPTFD YEMIFRGTGA LIYVIDAQDD YMEALTRLHI T VSKAYKVN PDMNFEVFIH KVDGLSDDHK IETQRDIHQR ANDDLADAGL EKLHLSFYLT SIYDHSIFEA FSKVVQKLIP QL PTLENLL NIFISNSGIE KAFLFDVVSK IYIATDSSPV DMQSYELCCD MIDVVIDVSC IYGLKEDGSG SAYDKESMAI IKL NNTTVL YLKEVTKFLA LVCILREESF ERKGLIDYNF HCFRKAIHEV FEVGVTSHRS CGHQTSASSL KALTHNGTPR NAI

UniProtKB: Ras-related GTP-binding protein C

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Macromolecule #6: Ragulator complex protein LAMTOR1

MacromoleculeName: Ragulator complex protein LAMTOR1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.762775 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MGCCYSSENE DSDQDREERK LLLDPSSPPT KALNGAEPNY HSLPSARTDE QALLSSILAK TASNIIDVSA ADSQGMEQHE YMDRARQYS TRLAVLSSSL THWKKLPPLP SLTSQPHQVL ASEPIPFSDL QQVSRIAAYA YSALSQIRVD AKEELVVQFG I P

UniProtKB: Ragulator complex protein LAMTOR1

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Macromolecule #7: Ragulator complex protein LAMTOR2

MacromoleculeName: Ragulator complex protein LAMTOR2 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.51745 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MLRPKALTQV LSQANTGGVQ STLLLNNEGS LLAYSGYGDT DARVTAAIAS NIWAAYDRNG NQAFNEDNLK FILMDCMEGR VAITRVANL LLCMYAKETV GFGMLKAKAQ ALVQYLEEPL TQVAAS

UniProtKB: Ragulator complex protein LAMTOR2

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Macromolecule #8: Ragulator complex protein LAMTOR3

MacromoleculeName: Ragulator complex protein LAMTOR3 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.637678 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MADDLKRFLY KKLPSVEGLH AIVVSDRDGV PVIKVANDNA PEHALRPGFL STFALATDQG SKLGLSKNKS IICYYNTYQV VQFNRLPLV VSFIASSSAN TGLIVSLEKE LAPLFEELRQ VVEVS

UniProtKB: Ragulator complex protein LAMTOR3

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Macromolecule #9: Ragulator complex protein LAMTOR4

MacromoleculeName: Ragulator complex protein LAMTOR4 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.753236 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MTSALTQGLE RIPDQLGYLV LSEGAVLASS GDLENDEQAA SAISELVSTA CGFRLHRGMN VPFKRLSVVF GEHTLLVTVS GQRVFVVKR QNRGREPIDV

UniProtKB: Ragulator complex protein LAMTOR4

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Macromolecule #10: Ragulator complex protein LAMTOR5

MacromoleculeName: Ragulator complex protein LAMTOR5 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.6229 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MEATLEQHLE DTMKNPSIVG VLCTDSQGLN LGCRGTLSDE HAGVISVLAQ QAAKLTSDPT DIPVVCLESD NGNIMIQKHD GITVAVHKM AS

UniProtKB: Ragulator complex protein LAMTOR5

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Macromolecule #11: Transcription factor EB

MacromoleculeName: Transcription factor EB / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.926621 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASRIGLRMQ LMREQAQQEE QRERMQQQAV MHYMQQQQQQ QQQQLGGPPT PAINTPVHFQ SPPPVPGEVL KVQSYLENPT SYHLQQSQH QKVREYLSET YGNKFAAHIS PAQGSPKPPP AASPGVRAGH VLSSSAGNSA PNSPMAMLHI GSNPERELDD V IDNIMRLD ...String:
MASRIGLRMQ LMREQAQQEE QRERMQQQAV MHYMQQQQQQ QQQQLGGPPT PAINTPVHFQ SPPPVPGEVL KVQSYLENPT SYHLQQSQH QKVREYLSET YGNKFAAHIS PAQGSPKPPP AASPGVRAGH VLSSSAGNSA PNSPMAMLHI GSNPERELDD V IDNIMRLD DVLGYINPEM QMPNTLPLSS SHLNVYSSDP QVTASLVGVT SSSCPADLTQ KRELTDAESR ALAKERQKKD NH NLIERRR RFNINDRIKE LGMLIPKAND LDVRWNKGTI LKASVDYIRR MQKDLQKSRE LENHSRRLEM TNKQLWLRIQ ELE MQARVH GLPTTSPSGM NMAELAQQVV KQELPSEEGP GEALMLGAEV PDPEPLPALP PQAPLPLPTQ PPSPFHHLDF SHSL SFGGR EDEGPPGYPE PLAPGHGSPF PSLSKKDLDL MLLDDSLLPL ASDPLLSTMS PEASKASSRR SSFSMEEGDV L

UniProtKB: Transcription factor EB

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Macromolecule #12: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 12 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #13: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #14: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 14 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #15: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 15 / Number of copies: 2 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: ab-initio reconstruction by cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 192332
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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