2023-03-29 REL PDBe PDBe PDBe 2021-09-17 2023-01-18 2023-01-18 2023-03-29 European Research Council (ERC) 834394 Switzerland Swiss National Science Foundation 179517 Switzerland H2020 Marie Curie Actions of the European Commission 789385 France European Research Council (ERC) 64778 France Helical reconstruction of TOROID (TORC1 Organized in Inhibited Domains) filaments. Felix J Prouteau M Bourgoint C Bonnadei L Desfosses A Gabus C Sadian Y Savvides SN Gutsche I Loewith R 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 associated EM volume TORC1 Organized in Inhibited Domains (TOROID) TORC1 Organized in Inhibited Domains (TOROID) 0 1 2 3 Saccharomyces cerevisiae Target of rapamycin complex 1 subunit KOG1 Saccharomyces cerevisiae
S. cerevisiae TOROIDs (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873), Lst8 (P41318) and Tor2 (P32600).
LEVO MPEIYGPQPLKPLNTVMRHGFEEQYQSDQLLQSLANDFIFYFDDKRHKTNGNPIPEEDKQ RDVNRYYQPITDWKIMKDRQKTVSAALLLCLNLGVDPPDVMKTHPCARVEAWVDPLNFQD SKKAIEQIGKNLQAQYETLSLRTRYKQSLDPCVEDVKRFCNSLRRTSKEDRILFHYNGHG VPKPTKSGEIWVFNRGYTQYIPVSLYDLQTWLGAPCIFVYDCNSAENILINFQKFVQKRI KDDEEGNHDVAAPSPTSAYQDCFQLASCTSDELLLMSPELPADLFSCCLTCPIEISIRIF LMQSPLKDSKYKIFFENSTSNQPFGDSKNSFKSKIPNVNIPGMLSDRRTPLGELNWIFTA ITDTIAWTSLPRPLFKKLFRHDLMIAALFRNFLLAKRIMPWYNCHPVSDPELPDSITTHP MWKSWDLAMDEVLTKIVIDLKNAPPATALESQMILQQQETLQNGGSSKSNAQDTKAGSIQ TQSRFAVANLSTMSLVNNPALQSRKSISLQSSQQQLQQQQQQQQQFTGFFEQNLTAFELW LKYASNVRHPPEQLPIVLQVLLSQVHRIRALVLLSRFLDLGPWAVYLSLSIGIFPYVLKL LQSPAPELKPILVFIWARIMSIDYKNTQSELIKEKGYMYFVTVLVPDWGVNGMSATNGSA MINSGNPLTMTASQNINGPSSRYYERQQGNRTSNLGHNNLPFYHSNDTTDEQKAMAVFVL ASFVRNFPLGQKNCFSLELVNKLCFYIDNSEIPLLRQWCVILLGLLFADNPLNRFVCMNT GAVEILLKSLKDPVPEVRTASIFALKHFISGFQDAEVILRLQQEFEEQYQQLHSQLQHLQ NQSHLQQQQSQQQQQHLEQQQMKIEKQIRHCQVMQNQLEVIDLRKLKRQEIGNLISILPL INDGSSLVRKELVVYFSHIVSRYSNFFIVVVFNDLLEEIKLLEKSDINTRNTSDKYSVSQ GSIFYTVWKSLLILAEDPFLENKELSKQVIDYILLELSAHKELGGPFAVMEKFLLKRSSK AHQTGKFGFNSSQVQFVKSSLRSFSPNERVDNNAFKKEQQQHDPKISHPMRTSLAKLFQS LGFSESNSDSDTQSSNTSMKSHTSKKGPSGLYLLNGNNNIYPTAETPRFRKHTEPLQLPL NSSFLDYSREYFQEPQMKKQEADEPGSVEYNARLWRRNRNETIIQETQGEKKLSIYGNWS KKLISLNNKSQPKLMKFAQFEDQLITADDRSTITVFDWEKGKTLSKFSNGTPFGTKVTDL KLINEDDSALLLTGSSDGVIKIYRDYQDVDTFKIVSAWRGLTDMLLTPRSTGLLTEWLQI RGSLLTTGDVKVIRVWDAHTETVEVDIPAKTSSLITSLTADQLAGNIFVAGFADGSLRVY DRRLDPRDSMIRRWRAGNDKQGVWINNVHLQRGGYRELVSGATNGVVELWDIRSEDPVES FVDQNVTSQYGSQQKPTTMTCMQVHEHAPIIATGTKQIKIWTTSGDLLNSFKNSHNNGVT STLAATGIPKSLSYSSTSDAFLSSMAFHPHRMMIAATNSHDSIVNIYKCEDERIDYF Serine/threonine-protein kinase TOR2 Saccharomyces cerevisiae
S. cerevisiae TOROIDs (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873), Lst8 (P41318) and Tor2 (P32600).
LEVO MNKYINKYTTPPNLLSLRQRAEGKHRTRKKLTHKSHSHDDEMSTTSNTDSNHNGPNDSGR VITGSAGHIGKISFVDSELDTTFSTLNLIFDKLKSDVPQERASGANELSTTLTSLAREVS AEQFQRFSNSLNNKIFELIHGFTSSEKIGGILAVDTLISFYLSTEELPNQTSRLANYLRV LIPSSDIEVMRLAANTLGRLTVPGGTLTSDFVEFEVRTCIDWLTLTADNNSSSSKLEYRR HAALLIIKALADNSPYLLYPYVNSILDNIWVPLRDAKLIIRLDAAVALGKCLTIIQDRDP ALGKQWFQRLFQGCTHGLSLNTNDSVHATLLVFRELLSLKAPYLRDKYDDIYKSTMKYKE YKFDVIRREVYAILPLLAAFDPAIFTKKYLDRIMVHYLRYLKNIDMNAANNSDKPFILVS IGDIAFEVGSSISPYMTLILDNIREGLRTKFKVRKQFEKDLFYCIGKLACALGPAFAKHL NKDLLNLMLNCPMSDHMQETLMILNEKIPSLESTVNSRILNLLSISLSGEKFIQSNQYDF NNQFSIEKARKSRNQSFMKKTGESNDDITDAQILIQCFKMLQLIHHQYSLTEFVRLITIS YIEHEDSSVRKLAALTSCDLFIKDDICKQTSVHALHSVSEVLSKLLMIAITDPVAEIRLE ILQHLGSNFDPQLAQPDNLRLLFMALNDEIFGIQLEAIKIIGRLSSVNPAYVVPSLRKTL LELLTQLKFSNMPKKKEESATLLCTLINSSDEVAKPYIDPILDVILPKCQDASSAVASTA LKVLGELSVVGGKEMTRYLKELMPLIINTFQDQSNSFKRDAALTTLGQLAASSGYVVGPL LDYPELLGILINILKTENNPHIRRGTVRLIGILGALDPYKHREIEVTSNSKSSVEQNAPS IDIALLMQGVSPSNDEYYPTVVIHNLMKILNDPSLSIHHTAAIQAIMHIFQNLGLRCVSF LDQIIPGIILVMRSCPPSQLDFYFQQLGSLISIVKQHIRPHVEKIYGVIREFFPIIKLQI TIISVIESISKALEGEFKRFVPETLTFFLDILENDQSNKRIVPIRILKSLVTFGPNLEDY SHLIMPIVVRMTEYSAGSLKKISIITLGRLAKNINLSEMSSRIVQALVRILNNGDRELTK ATMNTLSLLLLQLGTDFVVFVPVINKALLRNRIQHSVYDQLVNKLLNNECLPTNIIFDKE NEVPERKNYEDEMQVTKLPVNQNILKNAWYCSQQKTKEDWQEWIRRLSIQLLKESPSACL RSCSSLVSVYYPLARELFNASFSSCWVELQTSYQEDLIQALCKALSSSENPPEIYQMLLN LVEFMEHDDKPLPIPIHTLGKYAQKCHAFAKALHYKEVEFLEEPKNSTIEALISINNQLH QTDSAIGILKHAQQHNELQLKETWYEKLQRWEDALAAYNEKEAAGEDSVEVMMGKLRSLY ALGEWEELSKLASEKWGTAKPEVKKAMAPLAAGAAWGLEQWDEIAQYTSVMKSQSPDKEF YDAILCLHRNNFKKAEVHIFNARDLLVTELSALVNESYNRAYNVVVRAQIIAELEEIIKY KKLPQNSDKRLTMRETWNTRLLGCQKNIDVWQRILRVRSLVIKPKEDAQVRIKFANLCRK SGRMALAKKVLNTLLEETDDPDHPNTAKASPPVVYAQLKYLWATGLQDEALKQLINFTSR MAHDLGLDPNNMIAQSVPQQSKRVPRHVEDYTKLLARCFLKQGEWRVCLQPKWRLSNPDS ILGSYLLATHFDNTWYKAWHNWALANFEVISMLTSVSKKKQEGSDASSVTDINEFDNGMI GVNTFDAKEVHYSSNLIHRHVIPAIKGFFHSISLSESSSLQDALRLLTLWFTFGGIPEAT QAMHEGFNLIQIGTWLEVLPQLISRIHQPNQIVSRSLLSLLSDLGKAHPQALVYPLMVAI KSESLSRQKAALSIIEKMRIHSPVLVDQAELVSHELIRMAVLWHEQWYEGLDDASRQFFG EHNTEKMFAALEPLYEMLKRGPETLREISFQNSFGRDLNDAYEWLMNYKKSKDVSNLNQA WDIYYNVFRKIGKQLPQLQTLELQHVSPKLLSAHDLELAVPGTRASGGKPIVKISKFEPV FSVISSKQRPRKFCIKGSDGKDYKYVLKGHEDIRQDSLVMQLFGLVNTLLQNDAECFRRH LDIQQYPAIPLSPKSGLLGWVPNSDTFHVLIREHREAKKIPLNIEHWVMLQMAPDYDNLT LLQKVEVFTYALNNTEGQDLYKVLWLKSRSSETWLERRTTYTRSLAVMSMTGYILGLGDR HPSNLMLDRITGKVIHIDFGDCFEAAILREKFPEKVPFRLTRMLTYAMEVSGIEGSFRIT CENVMKVLRDNKGSLMAILEAFAFDPLINWGFDLPTKKIEEETGIQLPVMNANELLSNGA ITEEEVQRVENEHKNAIRNARAMLVLKRITDKLTGNDIRRFNDLDVPEQVDKLIQQATSV ENLCQHYIGWCPFW Target of rapamycin complex subunit LST8 Saccharomyces cerevisiae
S. cerevisiae TOROIDs (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873), Lst8 (P41318) and Tor2 (P32600).
LEVO MSVILVSAGYDHTIRFWEALTGVCSRTIQHSDSQVNRLEITNDKKLLATAGHQNVRLYDI RTTNPNPVASFEGHRGNVTSVSFQQDNRWMVTSSEDGTIKVWDVRSPSIPRNYKHNAPVN EVVIHPNQGELISCDRDGNIRIWDLGENQCTHQLTPEDDTSLQSLSMASDGSMLAAANTK GNCYVWEMPNHTDASHLKPVTKFRAHSTYITRILLSSDVKHLATCSADHTARVWSIDDDF KLETTLDGHQRWVWDCAFSADSAYLVTASSDHYVRLWDLSTREIVRQYGGHHKGAVCVAL NDV helical 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 Protease Inhibitor Cocktail 1.0 PMSF phenylmethylsulfonyl fluoride
50 mM MES-NaOH pH 6.0, 5 mM CHAPS, 600 mM KCl, 0,5 mM DTT, Phosphatase Inhibitor Mix, Complete Protease Inhibitor Cocktail (Roche; 1 tablet/ 50 ml) and 1 mM PMSF)
 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
Motion correction and dose weighting of the recorded movies were performed using MotionCor2, discarding the first frame.
26.7 47.32 D1 9.1 FSC 0.143 CUT-OFF RELION 2.0 Helical reconstruction 219455 219455 EMAN2 e2helixboxer module
A total of 219,455 particles (filaments) were extracted in RELION 2.0 using the --helix option, with an extract size of 600 pixels (810 Angstrom), an outer diameter of 620 Angstrom, and a helical rise of 26.75 Angstrom.
 EMD-3814
Map was low-pass filtered to 30 Angstrom.
 MAXIMUM LIKELIHOOD RELION 2.0 Helical reconstruction emd_13595.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 810.0 810.0 810.0 90.0 90.0 90.0 X Y Z -0.040822297 0.086129285 0.0020309312 0.0068145893 2.7 2.7 2.7 0.028 AUTHOR Helical reconstruction of TOROID (TORC1 Organized in Inhibited Domains) filaments. RIGID BODY FIT emd_13595_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 810.0 810.0 810.0 90.0 90.0 90.0 X Y Z -0.013787031 0.046307847 1.1877444e-05 0.006976776 2.7 2.7 2.7 AUTHOR Helical reconstruction of TOROID (TORC1 Organized in Inhibited Domains) filaments, half map 2. emd_13595_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 810.0 810.0 810.0 90.0 90.0 90.0 X Y Z -0.014034066 0.046088018 1.6287344e-05 0.0070211715 2.7 2.7 2.7 AUTHOR Helical reconstruction of TOROID (TORC1 Organized in Inhibited Domains) filaments, half map 1.