Human GATOR2 complex

2024-11-20 REL RCSB RCSB RCSB 2022-03-27 2022-07-20 2022-07-20 2024-11-20 National Institutes of Health/National Cancer Institute (NIH/NCI) K99 CA255926 United States Tuberous Sclerosis Association 2018-F01 United States Other private Charles King Trust Lustgarten Foundation United States Department of Defense (DOD, United States) TS200035 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) T32 GM007753 United States National Institutes of Health/National Cancer Institute (NIH/NCI) F30 CA228229 United States National Institutes of Health/National Cancer Institute (NIH/NCI) F31 CA180271 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) F31 GM121093 United States Other private Koch Institute Graduate Fellowship National Institutes of Health/National Cancer Institute (NIH/NCI) R01 CA103866 United States National Institutes of Health/National Cancer Institute (NIH/NCI) R01 CA129105 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01 AI047389 United States Department of Defense (DOD, United States) W81XWH-21-1-0260 United States Other private Leo Foundation American Cancer Society United States Howard Hughes Medical Institute (HHMI) United States Human GATOR2 complex Rogala KB Valenstein ML Lalgudi PV mTOR, GATOR, lysosome, nutrient sensing, complex, zinc finger, ZnF, RING, C2 symmetry, octagon, SIGNALING PROTEIN Valenstein ML Rogala KB Lalgudi PV Brignole EJ Gu X Saxton RA Chantranupong L Kolibius J Quast JP Sabatini DM Structure of the nutrient-sensing hub GATOR2. Nature UK 607 610 616 2022 35831510 doi:10.1038/s41586-022-04939-z 1476-4687 0006 NATUAS 7uhy FULLOVERLAP Human GATOR2 Human GATOR2 0 1 2 3 4 5 6 7

Purified five-component GATOR2 complex via a Flag-tag on MIOS.

Homo sapiens 1.1 GATOR complex protein MIOS Homo sapiens 0.10063338299999999 2 Homo sapiens LEVO MEMDYKDDDDKGGGGGASTMSGTKPDILWAPHHVDRFVVCDSELSLYHVESTVNSELKAGSLRLSEDSAATLLSINSDTP YMKCVAWYLNYDPECLLAVGQANGRVVLTSLGQDHNSKFKDLIGKEFVPKHARQCNTLAWNPLDSNWLAAGLDKHRADFS VLIWDICSKYTPDIVPMEKVKLSAGETETTLLVTKPLYELGQNDACLSLCWLPRDQKLLLAGMHRNLAIFDLRNTSQKMF VNTKAVQGVTVDPYFHDRVASFYEGQVAIWDLRKFEKPVLTLTEQPKPLTKVAWCPTRTGLLATLTRDSNIIRLYDMQHT PTPIGDETEPTIIERSVQPCDNYIASFAWHPTSQNRMIVVTPNRTMSDFTVFERISLAWSPITSLMWACGRHLYECTEEE NDNSLEKDIATKMRLRALSRYGLDTEQVWRNHILAGNEDPQLKSLWYTLHFMKQYTEDMDQKSPGNKGSLVYAGIKSIVK SSLGMVESSRHNWSGLDKQSDIQNLNEERILALQLCGWIKKGTDVDVGPFLNSLVQEGEWERAAAVALFNLDIRRAIQIL NEGASSEKGDLNLNVVAMALSGYTDEKNSLWREMCSTLRLQLNNPYLCVMFAFLTSETGSYDGVLYENKVAVRDRVAFAC KFLSDTQLNRYIEKLTNEMKEAGNLEGILLTGLTKDGVDLMESYVDRTGDVQTASYCMLQGSPLDVLKDERVQYWIENYR NLLDAWRFWHKRAEFDIHRSKLDPSSKPLAQVFVSCNFCGKSISYSCSAVPHQGRGFSQYGVSGSPTKSKVTSCPGCRKP LPRCALCLINMGTPVSSCPGGTKSDEKVDLSKDKKLAQFNNWFTWCHNCRHGGHAGHMLSWFRDHAECPVSACTCKCMQL DTTGNLVPAETVQP Q9NXC5 GATOR complex protein WDR24 Homo sapiens 0.08832695299999999 1 Homo sapiens LEVO MEKMSRVTTALGGSVLTGRTMHCHLDAPANAISVCRDAAQVVVAGRSIFKIYAIEEEQFVEKLNLRVGRKPSLNLSCADV VWHQMDENLLATAATNGVVVTWNLGRPSRNKQDQLFTEHKRTVNKVCFHPTEAHVLLSGSQDGFMKCFDLRRKDSVSTFS GQSESVRDVQFSIRDYFTFASTFENGNVQLWDIRRPDRCERMFTAHNGPVFCCDWHPEDRGWLATGGRDKMVKVWDMTTH RAKEMHCVQTIASVARVKWRPECRHHLATCSMMVDHNIYVWDVRRPFVPAAMFEEHRDVTTGIAWRHPHDPSFLLSGSKD SSLCQHLFRDASQPVERANPEGLCYGLFGDLAFAAKESLVAAESGRKPYTGDRRHPIFFKRKLDPAEPFAGLASSALSVF ETEPGGGGMRWFVDTAERYALAGRPLAELCDHNAKVARELGRNQVAQTWTMLRIIYCSPGLVPTANLNHSVGKGGSCGLP LMNSFNLKDMAPGLGSETRLDRSKGDARSDTVLLDSSATLITNEDNEETEGSDVPADYLLGDVEGEEDELYLLDPEHAHP EDPECVLPQEAFPLRHEIVDTPPGPEHLQDKADSPHVSGSEADVASLAPVDSSFSLLSVSHALYDSRLPPDFFGVLVRDM LHFYAEQGDVQMAVSVLIVLGERVRKDIDEQTQEHWYTSYIDLLQRFRLWNVSNEVVKLSTSRAVSCLNQASTTLHVNCS HCKRPMSSRGWVCDRCHRCASMCAVCHHVVKGLFVWCQGCSHGGHLQHIMKWLEGSSHCPAGCGHLCEYS Q96S15 GATOR complex protein WDR59 Homo sapiens 0.109938391 1 Homo sapiens LEVO MAARWSSENVVVEFRDSQATAMSVDCLGQHAVLSGRRFLYIVNLDAPFEGHRKISRQSKWDIGAVQWNPHDSFAHYFAAS SNQRVDLYKWKDGSGEVGTTLQGHTRVISDLDWAVFEPDLLVTSSVDTYIYIWDIKDTRKPTVALSAVAGASQVKWNKKN ANCLATSHDGDVRIWDKRKPSTAVEYLAAHLSKIHGLDWHPDSEHILATSSQDNSVKFWDYRQPRKYLNILPCQVPVWKA RYTPFSNGLVTVMVPQLRRENSLLLWNVFDLNTPVHTFVGHDDVVLEFQWRKQKEGSKDYQLVTWSRDQTLRMWRVDSQM QRLCANDILDGVDEFIESISLLPEPEKTLHTEDTDHQHTASHGEEEALKEDPPRNLLEERKSDQLGLPQTLQQEFSLINV QIRNVNVEMDAADRSCTVSVHCSNHRVKMLVKFPAQYPNNAAPSFQFINPTTITSTMKAKLLKILKDTALQKVKRGQSCL EPCLRQLVSCLESFVNQEDSASSNPFALPNSVTPPLPTFARVTTAYGSYQDANIPFPRTSGARFCGAGYLVYFTRPMTMH RAVSPTEPTPRSLSALSAYHTGLIAPMKIRTEAPGNLRLYSGSPTRSEKEQVSISSFYYKERKSRRWKSKREGSDSGNRQ IKAAGKVIIQDIACLLPVHKSLGELYILNVNDIQETCQKNAASALLVGRKDLVQVWSLATVATDLCLGPKSDPDLETPWA RHPFGRQLLESLLAHYCRLRDVQTLAMLCSVFEAQSRPQGLPNPFGPFPNRSSNLVVSHSRYPSFTSSGSCSSMSDPGLN TGGWNIAGREAEHLSSPWGESSPEELRFGSLTYSDPRERERDQHDKNKRLLDPANTQQFDDFKKCYGEILYRWGLREKRA EVLKFVSCPPDPHKGIEFGVYCSHCRSEVRGTQCAICKGFTFQCAICHVAVRGSSNFCLTCGHGGHTSHMMEWFRTQEVC PTGCGCHCLLESTF Q6PJI9 Isoform B of Nucleoporin SEH1 Homo sapiens 0.046636289 3 Homo sapiens LEVO MFVARSIAADHKDLIHDVSFDFHGRRMATCSSDQSVKVWDKSESGDWHCTASWKTHSGSVWRVTWAHPEFGQVLASCSFD RTAAVWEEIVGESNDKLRGQSHWVKRTTLVDSRTSVTDVKFAPKHMGLMLATCSADGIVRIYEAPDVMNLSQWSLQHEIS CKLSCSCISWNPSSSRAHSPMIAVGSDDSSPNAMAKVQIFEYNENTRKYAKAETLMTVTDPVHDIAFAPNLGRSFHILAI ATKDVRIFTLKPVRKELTSSGGPTKFEIHIVAQFDNHNSQVWRVSWNITGTVLASSGDDGCVRLWKANYMDNWKCTGILK GNGSPVNGSSQQGTSNPSLGSTIPSLQNSLNGSSAGRYFFTPLDSPRAGSRWSSYAQLLPPPPPPLVEHSCDADTANLQY PHPRRRYLSRPLNPLPENEGI Q96EE3 Protein SEC13 homolog Homo sapiens 0.035578438 1 Homo sapiens LEVO MVSVINTVDTSHEDMIHDAQMDYYGTRLATCSSDRSVKIFDVRNGGQILIADLRGHEGPVWQVAWAHPMYGNILASCSYD RKVIIWREENGTWEKSHEHAGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQWEVKKINNAHTIGCNAVSWAP AVVPGSLIDHPSGQKPNYIKRFASGGCDNLIKLWKEEEDGQWKEEQKLEAHSDWVRDVAWAPSIGLPTSTIASCSQDGRV FIWTCDDASSNTWSPKLLHKFNDVVWHVSWSITANILAVSGGDNKVTLWKESVDGQWVCISDVNKGQGSVSASVTEGQQN EQ P55735 Unknown Homo sapiens 0.001294587 1 Homo sapiens LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) Unknown Homo sapiens 0.0006988540000000001 1 Homo sapiens LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) ZINC ION 6.5409e-05 16 ZN singleParticle particle 3.0 7.5 50.0 HEPES 150.0 sodium chloride 0.1 CHAPS 50.0 L-arginine 50.0 L-glutamate 2.0 magnesium chloride 2.0 dithiothreitol Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY GLOW DISCHARGE 120 AIR 1e-05 ETHANE 95 277 FEI VITROBOT MARK IV

95% pure, monodisperse protein complex. Partial loss of a few subunits observed. Contaminating CCT chaperonin present.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.8 2.0 81000.0 45779.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 4103 2.4 44.0

Movie stacks were recorded in super-resolution counting mode at the UMass Medical School's Cryo-EM Core Facility in Worcester, Massachusetts, USA. 30 frames per stack.

GATAN K3 BIOQUANTUM (6k x 4k) 2 28792 4.0 47.0

Movie stacks were recorded in super-resolution counting mode at MIT.nano in Cambridge, Massachusetts, USA. 30 frames per stack.

Movie frames were weighted according to electron dose and particle movement. Please note that the two datasets collected at (1) UMass and (2) MIT.nano were eventually pixel-size-matched and merged into a single dataset.

7237873

The reported particle number is the sum of particles from two datasets, including parallel picking strategies. See details in the methods section of Valenstein and Rogala et al (2022).

Ab initio map was generated using stochastic gradient descent methods.

5 C2 FOURIER SPACE 3.66 FSC 0.143 CUT-OFF cryoSPARC 3.2.0

Duplicate particles were removed.

784651 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.1 16 253807.0 RELION 3.1

Four parallel particle sets were classified in 3D (4 classes per set). Only classes containing the fully assembled GATOR2 complex were processed further.

emd_26519.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 Z Y X -8.325661999999999 78.298676 0.02805115 1.4866972 1.0922 1.0922 1.0922 3.0 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: COMPOSITE MAP. Sharpened. C2-pseudosymmetric. 4L9O B 1043-2298 PDB experimental model 3JRP A 3-1179 PDB experimental model 3F3F A 1-346 PDB experimental model 3F3F C 47-99 PDB experimental model OTHER

Most of the structure was built de novo in Coot. WD40 propellers were rebuilt after fitting either deposited PDB coordinates of homologous structures or predicted models from RoseTTAFold.

REAL 182.0 emd_26519_msk_6.map emd_26519_msk_5.map emd_26519_msk_4.map emd_26519_msk_3.map emd_26519_msk_2.map emd_26519_msk_1.map emd_26519_additional_13.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.6024922 1.2584239 0.0011878923 0.022257248 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: LOCAL MAP #5. Unsharpened. emd_26519_additional_12.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.0029966587 1.8818734 0.0005189566 0.01523532 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: LOCAL MAP #5. Sharpened. emd_26519_additional_11.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.0018009552 1.7605954 0.0005160753 0.01548292 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: LOCAL MAP #3. Sharpened. From C2-symmetry expanded particles. emd_26519_additional_10.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.0017700774 1.9422855 0.000576434 0.017491942 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: LOCAL MAP #4. Sharpened. From C2-symmetry expanded particles. emd_26519_additional_9.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.5170444 1.6064906 0.0016787957 0.030067 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: LOCAL MAP #4. Unsharpened. From C2-symmetry expanded particles. emd_26519_additional_8.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.66473943 1.643847 0.0023023244 0.034042384 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: LOCAL MAP #3. Unsharpened. From C2-symmetry expanded particles. emd_26519_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.0018129456 2.0361683 0.00066915253 0.018121466 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: LOCAL MAP #2. Sharpened. From C2-symmetry expanded particles. emd_26519_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -1.3694594 2.7356625 0.0015634188 0.024503136 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: LOCAL MAP #1. Unsharpened. From C2-symmetry expanded particles. emd_26519_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.0017996985 2.2464879 0.00041046264 0.014691244 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: LOCAL MAP #1. Sharpened. From C2-symmetry expanded particles. emd_26519_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.60828537 1.4113805 0.0019968704 0.03458241 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: LOCAL MAP #2. Unsharpened. From C2-symmetry expanded particles. emd_26519_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.4318751 1.2179337 0.001583376 0.032890663 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: GLOBAL MAP. Unsharpened. C2-symmetric. emd_26519_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.0019757296 1.9324454 0.0013892024 0.025234096 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: GLOBAL MAP. Sharpened. C2-symmetric. emd_26519_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 Z Y X -17.014961 42.296970000000002 0.026067227 1.4275581 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: COMPOSITE MAP. Unsharpened. C2-pseudosymmetric. Used for the final refinement. emd_26519_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.43717793 1.2513261 0.0013581356 0.03853845 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: GLOBAL HALF-MAP A. C2-symmetric. emd_26519_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 419.40482 419.40482 419.40482 90.0 90.0 90.0 X Y Z -0.4611368 1.2989119 0.0013644645 0.03851397 1.0922 1.0922 1.0922 AUTHOR ::::EMDATABANK.org::::EMD-26519:::: GLOBAL HALF-MAP B. C2-symmetric.