Cryo-EM Structure of the Lysosomal Folliculin Complex (FLCN-FNIP2-RagA-RagC-Ragulator)

2024-11-20 REL RCSB RCSB RCSB 2019-02-13 2019-02-20 2019-11-06 2024-11-20 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 2R01GM111730-05 United States Cryo-EM Structure of the Lysosomal Folliculin Complex (FLCN-FNIP2-RagA-RagC-Ragulator) Fromm SA Young LN Hurley JH Lysosome, mTORC1 regulation, Amino acid sensing, GTPase, SIGNALING PROTEIN, signaling protein-inhibitor complex Lawrence RE Fromm SA Fu Y Yokom AL Kim DJ Thelen AM Young LN Lim CY Samelson AJ Hurley JH Zoncu R Structural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complex. Science US 366 971 977 2019 31672913 doi:10.1126/science.aax0364 1095-9203 0038 SCIEAS EMD-0556 other EM volume 6nzd FULLOVERLAP FLCN-FNIP2-RagA-RagC-Ragulator Complex FLCN-FNIP2-RagA-RagC-Ragulator Complex 0 1 2 3 4 5 6 7 8 9

RagA bound to GDP; RagC bound to XTPgammaS

Homo sapiens 0.34 Ragulator complex protein LAMTOR1 Homo sapiens 0.018325349999999997 1 Spodoptera frugiperda LEVO SNAEFMACCYSSENEDSDQDREERKLLLDPSSPPTKALNGAEPNYHSLPSARTDEQALLSSILAKTASNIIDVSAADSQG MEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELV VQFGIP Q6IAA8 Ragulator complex protein LAMTOR2 Homo sapiens 0.013645579 1 Spodoptera frugiperda LEVO GAMLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQAFNEDNLKFILMDCME GRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLTQVAAS Q9Y2Q5 Ragulator complex protein LAMTOR3 Homo sapiens 0.013637677999999999 1 Spodoptera frugiperda LEVO MADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALATDQGSKLGLSKNKSIICYYNTYQV VQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEELRQVVEVS Q9UHA4 Ragulator complex protein LAMTOR4 Homo sapiens 0.010753236000000001 1 Spodoptera frugiperda LEVO MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMNVPFKRLSVVFGEHTLLVTVS GQRVFVVKRQNRGREPIDV Q0VGL1 Hepatitis B virus x interacting protein Homo sapiens 0.01817852 1 Spodoptera frugiperda LEVO MEPGAGHLDGHRAGSPSLRQALCDGSAVMFSSKERGRCTVINFVPLEAPLRSTPRSRQVTEACGGEGRAVPLGSEPEWSV GGMEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPTDIPVVCLESDNGNIMIQK HDGITVAVHKMAS A0A0C4DGV4 Ras-related GTP-binding protein A Homo sapiens 0.036615168 1 Spodoptera frugiperda LEVO MPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFMENYFTSQRDN IFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACF RTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKL SCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKLERVDGPKHSLLMR Q7L523 Ras-related GTP-binding protein C Homo sapiens 0.044758336 1 Spodoptera frugiperda LEVO GADSRMSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPGGADSSKPRILLMGLRRSGKS SIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVNFQIWDFPGQMDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALT RLHITVSKAYKVNPDMNFEVFIHKVNGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQK LIPQLPTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYGLKEDGSGSAYDKESM AIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFRKAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTP RNAI Q9HB90 Folliculin Homo sapiens 0.06914307 1 Homo sapiens LEVO MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMNAIVALCHFCELHGPRTLFCTEVLHAPLPQGDGNED SPGQGEQAEEEEGGIQMNSRMRAHSPAEGASVESSSPGPKKSDMCEGCRSLAAGHPGYISHDKETSIKYVSHQHPSHPQL FSIVRQACVRSLSCEVCPGREGPIFFGDEQHGFVFSHTFFIKDSLARGFQRWYSIITIMMDRIYLINSWPFLLGKVRGII DELQGKALKVFEAEQFGCPQRAQRMNTAFTPFLHQRNGNAARSLTSLTSDDNLWACLHTSFAWLLKACGSRLTEKLLEGA PTEDTLVQMEKLADLEEESESWDNSEAEEEEKAPVLPESTEGRELTQGPAESSSLSGCGSWQPRKLPVFKSLRHMRQVLG APSFRMLAWHVLMGNQVIWKSRDVDLVQSAFEVLRTMLPVGCVRIIPYSSQYEEAYRCNFLGLSPHVQIPPHVLSSEFAV IVEVHAAARSTLHPVGCEDDQSLSKYEFVVTSGSPVAADRVGPTILNKIEAALTNQNLSVDVVDQCLVCLKEEWMNKVKV LFKFTKVDSRPKEDTQKLLSILGASEEDNVKLLKFWMTGLSKTYKSHLMSTVRSPTASESRN Q8NFG4 Folliculin-interacting protein 2 Homo sapiens 0.122475414 1 Homo sapiens LEVO GGTMAPTLLQKLFNKRGSSGSSAAASAQGRAPKEGPAFSWSCSEFDLNEIRLIVYQDCDRRGRQVLFDSKAVQKIEEVTA QKTEDVPIKISAKCCQGSSSVSSSSSSSISSHSSSGGSSHHAKEQLPKYQYTRPASDVNMLGEMMFGSVAMSYKGSTLKI HYIRSPPQLMISKVFSARMGSFCGSTNNLQDSFEYINQDPNLGKLNTNQNSLGPCRTGSNLAHSTPVDMPSRGQNEDRDS GIARSASLSSLLITPFPSPSSSTSSSSSYQRRWLRSQTTSLENGIIPRRSTDETFSLAEETCSSNPAMVRRKKIAISIIF SLCEKEEAQRNFQDFFFSHFPLFESHMNRLKSAIEKAMISCRKIAESSLRVQFYVSRLMEALGEFRGTIWNLYSVPRIAE PVWLTMMSGTLEKNQLCQRFLKEFTLLIEQINKNQFFAALLTAVLTYHLAWVPTVMPVDHPPIKAFSEKRTSQSVNMLAK THPYNPLWAQLGDLYGAIGSPVRLTRTVVVGKQKDLVQRILYVLTYFLRCSELQENQLTWSGNHGEGDQVLNGSKIITAL EKGEVEESEYVVITVRNEPALVPPILPPTAAERHNPWPTGFPECPEGTDSRDLGLKPDKEANRRPEQGSEACSAGCLGPA SDASWKPQNAFCGDEKNKEAPQDGSSRLPSCEVLGAGMKMDQQAVCELLKVEMPTRLPDRSVAWPCPDRHLREKPSLEKV TFQIGSFASPESDFESRMKKMEERVKACGPSLEASEAADVAQDPQVSRSPFKPGFQENVCCPQNRLSEGDEGESDKGFAE DRGSRNDMAADIAGQLSHAADLGTASHGAGGTGGRRLEATRGLYVKAAEGPVLEPVAPRCVQRGPGLVAGANIPCGDDNK KANFRTEGDIPRNESSDSALGDSDDEACASAMLDLGHGGDRTGGSLEVELPLPRSQSISTQNVRNFGRSLLAGYCPTYMP DLVLHGTGSDEKLKQCLVADLVHTVHHPVLDEPIAEAVCIIADTDKWSVQVATSQRKVTDNMKLGQDVLVSSQVSSLLQS ILQLYKLHLPADFCIMHLEDRLQEMYLKSKMLSEYLRGHTRVHVKELGVVLGIESNDLPLLTAIASTHSPYVAQILL Q9P278 GUANOSINE-5'-DIPHOSPHATE 0.000443201 1 GDP 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione 0.000540231 1 L8S singleParticle particle 0.5 7.4 25.0 HEPES 130.0 NaCl sodium chloride 2.5 MgCl2 magnesium chloride 2.0 EGTA 0.5 TCEP C-flat-2/1 COPPER 300 CARBON HOLEY PLASMA CLEANING 12 OTHER

15 W

ETHANE 90 277 FEI VITROBOT MARK IV

Whatman 597.

FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 3.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 1 2703 11.0 65.6 1 982343

cryoSPARC v2 ab-initio

C1 3.6 FSC 0.143 CUT-OFF cryoSPARC 2 163376 NOT APPLICABLE NOT APPLICABLE emd_0554.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 413.64 413.64 413.64 90.0 90.0 90.0 X Y Z -0.36063316 0.79141235 0.00061260565 0.0105887605 1.149 1.149 1.149 0.16 AUTHOR ::::EMDATABANK.org::::D_1000239621:::: generated by non-uniform refinement from cryoSPARC v2 followed by LocScale amplitude scaling 6B9X A PDB experimental model 6B9X B PDB experimental model 6B9X C PDB experimental model 6B9X D PDB experimental model 6B9X E PDB experimental model 6EHR E 48-68 PDB experimental model 6CES A PDB experimental model 6CES C PDB experimental model 3V42 B PDB experimental model 3LLU A 119-139 PDB experimental model REAL emd_0554_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 413.64 413.64 413.64 90.0 90.0 90.0 X Y Z -2.5242438 4.1277614 0.0018420722 0.04121762 1.149 1.149 1.149 AUTHOR ::::EMDATABANK.org::::D_1000239621:::: generated by non-uniform refinement from cryoSPARC v2 followed by the cryoSPARC v2 local filtering/sharpening routine emd_0554_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 413.64 413.64 413.64 90.0 90.0 90.0 X Y Z -1.6694148 3.1097076 0.00070766616 0.07048329 1.149 1.149 1.149 AUTHOR ::::EMDATABANK.org::::D_1000239621:::: generated by non-uniform refinement from cryoSPARC v2 followed by the Relion3-beta PostProcess routine