2024-10-23 REL PDBe PDBe PDBe 2021-09-17 2023-01-18 2023-01-18 2024-10-23 European Research Council (ERC) 834394 European Union Swiss National Science Foundation 179517 European Union H2020 Marie Curie Actions of the European Commission 789385 European Union European Research Council (ERC) 64778 European Union Cryo-EM structure of Saccharomyces cerevisiae TOROID (TORC1 Organized in Inhibited Domains). Felix J Prouteau M Bourgoint C Bonadei L Desfosses A Gabus C Sadian Y Savvides SN Gutsche I Loewith R TARGET OF RAPAMYCIN, TORC1, KOG1, LST8, TOR2, FRB DOMAIN, SIGNALING PROTEIN Prouteau M Bourgoint C Felix J Bonadei L Sadian Y Gabus C Savvides SN Gutsche I Desfosses A Loewith R EGOC inhibits TOROID polymerization by structurally activating TORC1. Nat.Struct.Mol.Biol. US 30 273 285 2023 36702972 doi:10.1038/s41594-022-00912-6 1545-9985 EMD-13595 other EM volume 7pqh FULLOVERLAP TORC1 Organized in Inhibited Domains (TOROID) TORC1 Organized in Inhibited Domains (TOROID) 0 1 2 3 Saccharomyces cerevisiae RL174-5b: MATa; TB50, KOG1::TAP-HIS3 tor1Delta::KanMX6 Target of rapamycin complex 1 subunit KOG1,Target of rapamycin complex 1 subunit Kog1 Saccharomyces cerevisiae 0.183594562
S. cerevisiae TOROIDS (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873) Lst8, P41318) and Tor2 (P32600),S. cerevisiae TOROIDS (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873) Lst8, P41318) and Tor2 (P32600)
4 Saccharomyces cerevisiae LEVO MPEIYGPQPLKPLNTVMRHGFEEQYQSDQLLQSLANDFIFYFDDKRHKTNGNPIPEEDKQRDVNRYYQPITDWKIMKDRQ KTVSAALLLCLNLGVDPPDVMKTHPCARVEAWVDPLNFQDSKKAIEQIGKNLQAQYETLSLRTRYKQSLDPCVEDVKRFC NSLRRTSKEDRILFHYNGHGVPKPTKSGEIWVFNRGYTQYIPVSLYDLQTWLGAPCIFVYDCNSAENILINFQKFVQKRI KDDEEGNHDVAAPSPTSAYQDCFQLASCTSDELLLMSPELPADLFSCCLTCPIEISIRIFLMQSPLKDSKYKIFFENSTS NQPFGDSKNSFKSKIPNVNIPGMLSDRRTPLGELNWIFTAITDTIAWTSLPRPLFKKLFRHDLMIAALFRNFLLAKRIMP WYNCHPVSDPELPDSITTHPMWKSWDLAMDEVLTKIVIDLKNAPPATALESQMILQQQETLQNGGSSKSNAQDTKAGSIQ TQSRFAVANLSTMSLVNNPALQSRKSISLQSSQQQLQQQQQQQQQFTGFFEQNLTAFELWLKYASNVRHPPEQLPIVLQV LLSQVHRIRALVLLSRFLDLGPWAVYLSLSIGIFPYVLKLLQSPAPELKPILVFIWARIMSIDYKNTQSELIKEKGYMYF VTVLVPDWGVNGMSATNGSAMINSGNPLTMTASQNINGPSSRYYERQQGNRTSNLGHNNLPFYHSNDTTDEQKAMAVFVL ASFVRNFPLGQKNCFSLELVNKLCFYIDNSEIPLLRQWCVILLGLLFADNPLNRFVCMNTGAVEILLKSLKDPVPEVRTA SIFALKHFISGFQDAEVILRLQQEFEEQYQQLHSQLQHLQNQSHLQQQQSQQQQQHLEQQQMKIEKQIRHCQVMQNQLEV IDLRKLKRQEIGNLISILPLINDGSSLVRKELVVYFSHIVSRYSNFFIVVVFNDLLEEIKLLEKSDINTRNTSDKYSVSQ GSIFYTVWKSLLILAEDPFLENKELSKQVIDYILLELSAHKELGGPFAVMEKFLLKRSSKAHQTGKFGFNSSQVQFVKSS LRSFSPNERVDNNAFKKEQQQHDPKISHPMRTSLAKLFQSLGFSESNSDSDTQSSNTSMKSHTSKKGPSGLYLLNGNNNI YPTAETPRFRKHTEPLQLPLNSSFLDYSREYFQEPQMKKQEADEPGSVEYNARLWRRNRNETIIQETQGEKKLSIYGNWS KKLISLNNKSQPKLMKFAQFEDQLITADDRSTITVFDWEKGKTLSKFSNGTPFGTKVTDLKLINEDDSALLLTGSSDGVI KIYRDYQDVDTFKIVSAWRGLTDMLLTPRSTGLLTEWLQIRGSLLTTGDVKVIRVWDAHTETVEVDIPAKTSSLITSLTA DQLAGNIFVAGFADGSLRVYDRRLDPRDSMIRRWRAGNDKQGVWINNVHLQRGGYRELVSGATNGVVELWDIRSEDPVES FVDQNVTSQYGSQQKPTTMTCMQVHEHAPIIATGTKQIKIWTTSGDLLNSFKNSHNNGVTSTLAATGIPKSLSYSSTSDA FLSSMAFHPHRMMIAATNSHDSIVNIYKCEDERIDYFRTLQVDKRRWKKNFIAVSAANRFKKISSSGALDYDIPTTASVD GSENLYFQ P38873 Target of rapamycin complex subunit LST8 Saccharomyces cerevisiae ATCC 204508 / S288c 0.034077879
S. cerevisiae TOROIDs (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873), Lst8 (P41318) and Tor2 (P32600)
4 Saccharomyces cerevisiae LEVO MSVILVSAGYDHTIRFWEALTGVCSRTIQHSDSQVNRLEITNDKKLLATAGHQNVRLYDIRTTNPNPVASFEGHRGNVTS VSFQQDNRWMVTSSEDGTIKVWDVRSPSIPRNYKHNAPVNEVVIHPNQGELISCDRDGNIRIWDLGENQCTHQLTPEDDT SLQSLSMASDGSMLAAANTKGNCYVWEMPNHTDASHLKPVTKFRAHSTYITRILLSSDVKHLATCSADHTARVWSIDDDF KLETTLDGHQRWVWDCAFSADSAYLVTASSDHYVRLWDLSTREIVRQYGGHHKGAVCVALNDV P41318 Serine/threonine-protein kinase TOR2 Saccharomyces cerevisiae ATCC 204508 / S288c 0.281915438
S. cerevisiae TOROIDs (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873), Lst8 (P41318) and Tor2 (P32600)
4 Saccharomyces cerevisiae LEVO MNKYINKYTTPPNLLSLRQRAEGKHRTRKKLTHKSHSHDDEMSTTSNTDSNHNGPNDSGRVITGSAGHIGKISFVDSELD TTFSTLNLIFDKLKSDVPQERASGANELSTTLTSLAREVSAEQFQRFSNSLNNKIFELIHGFTSSEKIGGILAVDTLISF YLSTEELPNQTSRLANYLRVLIPSSDIEVMRLAANTLGRLTVPGGTLTSDFVEFEVRTCIDWLTLTADNNSSSSKLEYRR HAALLIIKALADNSPYLLYPYVNSILDNIWVPLRDAKLIIRLDAAVALGKCLTIIQDRDPALGKQWFQRLFQGCTHGLSL NTNDSVHATLLVFRELLSLKAPYLRDKYDDIYKSTMKYKEYKFDVIRREVYAILPLLAAFDPAIFTKKYLDRIMVHYLRY LKNIDMNAANNSDKPFILVSIGDIAFEVGSSISPYMTLILDNIREGLRTKFKVRKQFEKDLFYCIGKLACALGPAFAKHL NKDLLNLMLNCPMSDHMQETLMILNEKIPSLESTVNSRILNLLSISLSGEKFIQSNQYDFNNQFSIEKARKSRNQSFMKK TGESNDDITDAQILIQCFKMLQLIHHQYSLTEFVRLITISYIEHEDSSVRKLAALTSCDLFIKDDICKQTSVHALHSVSE VLSKLLMIAITDPVAEIRLEILQHLGSNFDPQLAQPDNLRLLFMALNDEIFGIQLEAIKIIGRLSSVNPAYVVPSLRKTL LELLTQLKFSNMPKKKEESATLLCTLINSSDEVAKPYIDPILDVILPKCQDASSAVASTALKVLGELSVVGGKEMTRYLK ELMPLIINTFQDQSNSFKRDAALTTLGQLAASSGYVVGPLLDYPELLGILINILKTENNPHIRRGTVRLIGILGALDPYK HREIEVTSNSKSSVEQNAPSIDIALLMQGVSPSNDEYYPTVVIHNLMKILNDPSLSIHHTAAIQAIMHIFQNLGLRCVSF LDQIIPGIILVMRSCPPSQLDFYFQQLGSLISIVKQHIRPHVEKIYGVIREFFPIIKLQITIISVIESISKALEGEFKRF VPETLTFFLDILENDQSNKRIVPIRILKSLVTFGPNLEDYSHLIMPIVVRMTEYSAGSLKKISIITLGRLAKNINLSEMS SRIVQALVRILNNGDRELTKATMNTLSLLLLQLGTDFVVFVPVINKALLRNRIQHSVYDQLVNKLLNNECLPTNIIFDKE NEVPERKNYEDEMQVTKLPVNQNILKNAWYCSQQKTKEDWQEWIRRLSIQLLKESPSACLRSCSSLVSVYYPLARELFNA SFSSCWVELQTSYQEDLIQALCKALSSSENPPEIYQMLLNLVEFMEHDDKPLPIPIHTLGKYAQKCHAFAKALHYKEVEF LEEPKNSTIEALISINNQLHQTDSAIGILKHAQQHNELQLKETWYEKLQRWEDALAAYNEKEAAGEDSVEVMMGKLRSLY ALGEWEELSKLASEKWGTAKPEVKKAMAPLAAGAAWGLEQWDEIAQYTSVMKSQSPDKEFYDAILCLHRNNFKKAEVHIF NARDLLVTELSALVNESYNRAYNVVVRAQIIAELEEIIKYKKLPQNSDKRLTMRETWNTRLLGCQKNIDVWQRILRVRSL VIKPKEDAQVRIKFANLCRKSGRMALAKKVLNTLLEETDDPDHPNTAKASPPVVYAQLKYLWATGLQDEALKQLINFTSR MAHDLGLDPNNMIAQSVPQQSKRVPRHVEDYTKLLARCFLKQGEWRVCLQPKWRLSNPDSILGSYLLATHFDNTWYKAWH NWALANFEVISMLTSVSKKKQEGSDASSVTDINEFDNGMIGVNTFDAKEVHYSSNLIHRHVIPAIKGFFHSISLSESSSL QDALRLLTLWFTFGGIPEATQAMHEGFNLIQIGTWLEVLPQLISRIHQPNQIVSRSLLSLLSDLGKAHPQALVYPLMVAI KSESLSRQKAALSIIEKMRIHSPVLVDQAELVSHELIRMAVLWHEQWYEGLDDASRQFFGEHNTEKMFAALEPLYEMLKR GPETLREISFQNSFGRDLNDAYEWLMNYKKSKDVSNLNQAWDIYYNVFRKIGKQLPQLQTLELQHVSPKLLSAHDLELAV PGTRASGGKPIVKISKFEPVFSVISSKQRPRKFCIKGSDGKDYKYVLKGHEDIRQDSLVMQLFGLVNTLLQNDAECFRRH LDIQQYPAIPLSPKSGLLGWVPNSDTFHVLIREHREAKKIPLNIEHWVMLQMAPDYDNLTLLQKVEVFTYALNNTEGQDL YKVLWLKSRSSETWLERRTTYTRSLAVMSMTGYILGLGDRHPSNLMLDRITGKVIHIDFGDCFEAAILREKFPEKVPFRL TRMLTYAMEVSGIEGSFRITCENVMKVLRDNKGSLMAILEAFAFDPLINWGFDLPTKKIEEETGIQLPVMNANELLSNGA ITEEEVQRVENEHKNAIRNARAMLVLKRITDKLTGNDIRRFNDLDVPEQVDKLIQQATSVENLCQHYIGWCPFW P32600 2.7.1.67 singleParticle filament 0.02 7.5 50.0 MES-NaOH 2-(N-morpholino)ethanesulfonic acid-sodium hydroxide 5.0 CHAPS 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate 600.0 NaCl sodium chloride 0.5 DTT Dithiothreitol Phosphatase Inhibitor Mix 1.0 Complete Complete Protease Inhibitor Cocktail (Roche) 1.0 PMSF phenylmethylsulfonyl fluoride PELCO Ultrathin Carbon with Lacey Carbon GLOW DISCHARGE ETHANE HOMEMADE PLUNGER FEI TITAN KRIOS FLOOD BEAM OTHER FIELD EMISSION GUN 300 2.7 0.8 2.5 37000.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 2-16 4901 8.0 20.0 1 219455 EMD-3814 D2 3.87 FSC 0.143 CUT-OFF cryoSPARC 3.01
Based on an initial helical reconstruction in RELION2.0, we performed signal subtraction to generate a set of 219,455 subtracted particles containing one isolated Torc1 assembly per segment. Next, we employed the localrec module in Scipion to crop and re-center the signal subtracted particles in a smaller box of 300 pixels, as well as assigning to each particle a refined defocus based on the helical geometry. Single-particle analysis of the subtracted particles using 3D refinement in RELION2.0, while imposing D1 symmetry, resulted in a map with a resolution of 4.5 Angstrom (FSC = 0.143). We then imported the particles from the RELION2.0 refinement in cryoSPARC 3.01. After 2D classification and class selection, a set of 213808 selected particles was used for Non-Uniform refinement in cryoSPARC 3.01, employing a dynamic mask, imposing D1 symmetry, using the option to keep particles from the same helix in the same half-set, and allowing high-order aberration estimation and correction, which resulted in a final map with a resolution of 3.87 Angstrom (FSC = 0.143).
218872 MAXIMUM LIKELIHOOD RELION 2.0 MAXIMUM LIKELIHOOD cryoSPARC 3.01 cryoSPARC 3.01 emd_13594.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 405.0 405.0 405.0 90.0 90.0 90.0 X Y Z -0.057120483 2.3437147 0.0039005666 0.04260644 1.35 1.35 1.35 0.12 AUTHOR Main EM map of TORC1 in TOROID (TORC1 Organized in Inhibited Domains), obtained by Single Particle Analysis (SPA) after signal subtraction performed on TOROID filaments. OTHER
Initial homology models of Tor2 and Lst8 were generated using Phyre2, while a model of Kog1 was generated using ITasser. Homology models of Tor2, Lst8 and Kog1 were first manually placed in the final 3D map followed by rigid-body fitting in Chimera. The rigid-body fitted models were subsequently subjected to a round of flexible fitting using Imodfit followed by automatic molecular dynamics flexible fitting using NAMDINATOR. The flexibly fitted structure was then refined using the Phenix software package.
 emd_13594_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 405.0 405.0 405.0 90.0 90.0 90.0 X Y Z -0.4667202 1.1934117 0.0033611457 0.068430424 1.35 1.35 1.35 AUTHOR EM half map 2 of TORC1 in TOROID (TORC1 Organized in Inhibited Domains), obtained by Single Particle Analysis (SPA) after signal subtraction performed on TOROID filaments. emd_13594_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 405.0 405.0 405.0 90.0 90.0 90.0 X Y Z -0.43497193 1.2240461 0.0033644908 0.06852792 1.35 1.35 1.35 AUTHOR EM half map 1 of TORC1 in TOROID (TORC1 Organized in Inhibited Domains), obtained by Single Particle Analysis (SPA) after signal subtraction performed on TOROID filaments.