The structure of the COPI coat leaf in complex with the ArfGAP2 uncoating factor

2024-07-10 REL PDBe PDBe PDBe 2017-05-15 2017-05-31 2017-06-28 2024-07-10 German Research Foundation SFB638 (A16 and Z4) Germany German Research Foundation WI 654/12-1 Germany The structure of the COPI coat leaf in complex with the ArfGAP2 uncoating factor Dodonova SO Aderhold P COPI, coated vesicles, ArfGAP2, Transport protein Dodonova SO Aderhold P Kopp J Ganeva I Rohling S Hagen WJ Sinning I Wieland F Briggs JA 9 angstrom structure of the COPI coat reveals that the Arf1 GTPase occupies two contrasting molecular environments. Elife US 6 2017 28621666 doi:10.7554/eLife.26691 2050-084X 5nzs FULLOVERLAP The structure of the COPI coat leaf The structure of the COPI coat leaf 0 1 2 3 4 5 6 7

The asymmetric unit of the COPI coat

0.55 COPI coat complex 1 1 2 3 4 6 7 Mus musculus ADP-ribosylation factor 1 1 5 Saccharomyces cerevisiae ADP-ribosylation factor GTPase-activating protein 2 1 8 Rattus norvegicus Coatomer subunit alpha Mus musculus 0.14253274999999999

WSHPQFEK is a C-terminal Strep-Tag

1 Spodoptera frugiperda LEVO MLTKFETKSARVKGLSFHPKRPWILTSLHNGVIQLWDYRMCTLIDKFDEHDGPVRGIDFHKQQPLFVSGGDDYKIKVWNY KLRRCLFTLLGHLDYIRTTFFHHEYPWILSASDDQTIRVWNWQSRTCVCVLTGHNHYVMCAQFHPSEDLVVSASLDQTVR VWDISGLRKKNLSPGAVESDVRGITGVDLFGTTDAVVKHVLEGHDRGVNWAAFHPTMPLIVSGADDRQVKIWRMNESKAW EVDTCRGHYNNVSCAVFHPRQELILSNSEDKSIRVWDMSKRTGVQTFRRDHDRFWVLAAHPNLNLFAAGHDGGMIVFKLE RERPAYAVHGNMLHYVKDRFLRQLDFNSSKDVAVMQLRSGSKFPVFNMSYNPAENAVLLCTRASNLENSTYDLYTIPKDA DSQNPDAPEGKRSSGLTAVWVARNRFAVLDRMHSLLIKNLKNEITKKIQVPNCDEIFYAGTGNLLLRDADSITLFDVQQK RTLASVKISKVKYVIWSADMSHVALLAKHAIVICNRKLDALCNIHENIRVKSGAWDESGVFIYTTSNHIKYAVTTGDHGI IRTLDLPIYVTRVKGNNVYCLDRECRPRVLTIDPTEFKFKLALINRKYDEVLHMVRNAKLVGQSIIAYLQKKGYPEVALH FVKDEKTRFSLALECGNIEIALEAAKALDDKNCWEKLGEVALLQGNHQIVEMCYQRTKNFDKLSFLYLITGNLEKLRKMM KIAEIRKDMSGHYQNALYLGDVSERVRILKNCGQKSLAYLSAATHGLDEEAESLKETFDPEKETIPDIDPNAKLLQPPAP IMPLDTNWPLLTVSKGFFEGSIASKGKGGALAADIDIDTVGTEGWGEDAELQLDEDGFVEAPEGLGEDVLGKGQEEGGGW DVEEDLELPPELDVPSGVSGSAEDGFFVPPTKGTSPTQIWCNNSQLPVDHILAGSFETAMRLLHDQVGVIQFGPYKQLFL QTYARGRTTYQALPCLPSMYSYPNRNWKDAGLKNGVPAVGLKLNDLIQRLQLCYQLTTVGKFEEAVEKFRSILLSVPLLV VDNKQEIAEAQQLITICREYIVGLCMEIERKKLPKETLDQQKRICEMAAYFTHSNLQPVHMILVLRTALNLFFKLKNFKT AATFARRLLELGPKPEVAQQTRKILSACEKNPTDACQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEFKGQI CRVTTVTEIGKDVIGLRISPLQFRLEVLFQGPSAWSHPQFEKGGGSGGGSGGSAWSHPQFEK Q8CIE6 Coatomer subunit beta Mus musculus 0.109148109 1 Spodoptera frugiperda LEVO MHHHHHHENLYFQGHMTAAENVCYTLINVPMDSEPPSEISLKNDLEKGDVKSKTEALKKVIIMILNGEKLPGLLMTIIRF VLPLQDHTIKKLLLVFWEIVPKTTPDGRLLHEMILVCDAYRKDLQHPNEFIRGSTLRFLCKLKEAELLEPLMPAIRACLE HRHSYVRRNAVLAIYTIYRNFEHLIPDAPELIHDFLVNEKDASCKRNAFMMLIHADQDRALDYLSTCIDQVQTFGDILQL VIVELIYKVCHANPSERARFIRCIYNLLQSSSPAVKYEAAGTLVTLSSAPTAIKAAAQCYIDLIIKESDNNVKLIVLDRL VELKEHPAHERVLQDLVMDILRVLSTPDLEVRKKTLQLALDLVSSRNVEELVIVLKKEVIKTNNVSEHEDTDKYRQLLVR TLHSCSVRFPDMAANVIPVLMEFLSDSNEAAAADVLEFVREAIQRFDNLRMLIVEKMLEVFHAIKSVKIYRGALWILGEY CSTKEDIQSVMTEVRRSLGEIPIVESEIKKEAGELKPEEEITVGPVQKLVTEMGTYATQSALSSSRPTKKEEDRPPLRGF LLDGDFFVAASLATTLTKIALRYVALVQEKKKQNSFVAEAMLLMATILHLGKSSLPKKPITDDDVDRISLCLKVLSECSP LMNDIFNKECRQSLSQMLSAKLEEEKLSQKKESEKRNVTVQPDDPISFMQLTAKNEMNCKEDQFQLSLLAAMGNTQRKEA ADPLASKLNKVTQLTGFSDPVYAEAYVHVNQYDIVLDVLVVNQTSDTLQNCTLELATLGDLKLVEKPSPLTLAPHDFANI KANVKVASTENGIIFGNIVYDVSGAASDRNCVVLSDIHIDIMDYIQPATCTDAEFRQMWAEFEWENKVTVNTNMTDLNDY LQHILKSTNMKCLTPEKALSGYCGFMAANLYARSIFGEDALANVSIEKPVHQGPDAAVTGHIRIRAKSQGMALSLGDKIN LSQKKTSL Q9JIF7 Coatomer subunit beta' Mus musculus 0.10256607799999999 1 Spodoptera frugiperda LEVO MPLRLDIKRKLTARSDRVKSVDLHPTEPWMLASLYNGSVCVWNHETQTLVKTFEVCDLPVRAAKFVARKNWVVTGADDMQ IRVFNYNTLERVHMFEAHSDYIRCIAVHPTQPFILTSSDDMLIKLWDWDKKWSCSQVFEGHTHYVMQIVINPKDNNQFAS ASLDRTIKVWQLGSSSPNFTLEGHEKGVNCIDYYSGGDKPYLISGADDRLVKIWDYQNKTCVQTLEGHAQNVSCASFHPE LPIIITGSEDGTVRIWHSSTYRLESTLNYGMERVWCVASLRGSNNVALGYDEGSIIVKLGREEPAMSMDANGKIIWAKHS EVQQANLKAMGDTEIKDGERLPLAVKDMGSCEIYPQTIQHNPNGRFVVVCGDGEYIIYTAMALRNKSFGSAQEFAWAHDS SEYAIRESNSIVKIFKNFKEKKSFKPDFGAESIYGGFLLGVRSVNGLAFYDWENTELIRRIEIQPKHIFWSDSGELVCIA TEESFFILKYLSEKVLAAQETHEGVTEDGIEDAFEVLGEIQEIVKTGLWVGDCFIYTSSVNRLNYYVGGEIVTIAHLDRT MYLLGYIPKDNRLYLGDKELNIVSYSLLVSVLEYQTAVMRRDFSMADKVLPTIPKEQRTRVAHFLEKQGFKQQALTVSTD PEHRFELALQLGELKIAYQLAVEAESEQKWKQLAELAISKCQFSLAQECLHHAQDYGGLLLLATASGNASMVNKLAEGAE RDGKNNVAFMSYFLQGKLDACLELLIRTGRLPEAAFLARTYLPSQVSRVVKLWRENLSKVNQKAAESLADPTEYENLFPG LKEAFVVEEWVKETHADLWPAKQYPLVTPNEERNVMEEAKGFQPSRPTAQQEPDGKPASSPVIMASQTTHKEEKSLLELE VDLDNLELEDIDTTDINLDEDILDD O55029 Coatomer subunit delta Mus musculus 0.057304249999999994 1 Spodoptera frugiperda LEVO MVLLAAAVCTKAGKAIVSRQFVEMTRTRIEGLLAAFPKLMNTGKQHTFVETESVRYVYQPMEKLYMVLITTKNSNILEDL ETLRLFSRVIPEYCRALEENEISEHCFDLIFAFDEIVALGYRENVNLAQIRTFTEMDSHEEKVFRAVRETQEREAKAEMR RKAKELQQARRDAERQGKKAPGFGGFGSSAVSGGSTAAMITETIIETDKPKVAPAPARPSGPSKALKLGAKGKEVDNFVD KLKSEGETIMSSNMGKRTSEATKVHAPPINMESVHMKIEEKITLTCGRDGGLQNMELHGMIMLRISDDKFGRIRLHVENE DKKGVQLQTHPNVDKKLFTAESLIGLKNPEKSFPVNSDVGVLKWRLQTTEESFIPLTINCWPSESGNGCDVNIEYELQED NLELNDVVITIPLPSGVGAPVIGEIDGEYRHDSRRNTLEWCLPVIDAKNKSGSLEFSIPGQPNDFFPVQVSFISKKNYCN IQVTKVTQVDGNSPVRFSTETTFLVDKYEIL Q5XJY5 ADP-ribosylation factor 1 Saccharomyces cerevisiae 0.020552437999999996 3 Escherichia coli LEVO MGLFASKLFSNLFGNKEMRILMVGLDGAGKTTVLYKLKLGEVITTIPTIGFNVETVQYKNISFTVWDVGGQDRIRSLWRH YYRNTEGVIFVVDSNDRSRIGEAREVMQRMLNEDELRNAAWLVFANKQDLPEAMSAAEITEKLGLHSIRNRPWFIQATCA TSGEGLYEGLEWLSNSLKNST P11076 Coatomer subunit gamma-1 Mus musculus 0.09762270299999999 2 Spodoptera frugiperda LEVO MLKKFDKKDEESGGGSNPLQHLEKSAVLQEARVFNETPINPRKCAHILTKILYLINQGEHLGTTEATEAFFAMTKLFQSN DPTLRRMCYLTIKEMSCIAEDVIIVTSSLTKDMTGKEDNYRGPAVRALCQITDSTMLQAVERYMKQAIVDKVPSVSSSAL VSSLHLLKCSFDVVKRWVNEAQEAASSDNIMVQYHALGLLYHVRKNDRLAVSKMISKFTRHGLKSPFAYCMMIRVASKQL EEEDGSRDSPLFDFIESCLRNKHEMVVYEAASAIVNLPGCSAKELAPAVSVLQLFCSSPKAALRYAAVRTLNKVAMKHPS AVTACNLDLENLVTDSNRSIATLAITTLLKTGSESSIDRLMKQISSFMSEISDEFKVVVVQAISALCQKYPRKHAVLMNF LFTMLREEGGFEYKRAIVDCIISIIEENSESKETGLSHLCEFIEDCEFTVLATRILHLLGQEGPKTNNPSKYIRFIYNRV VLEHEEVRAGAVSALAKFGAQNEEMLPSILVLLKRCVMDDDNEVRDRATFYLNVLEQKQKALNAGYILNGLTVSIPGLEK ALQQYTLEPSEKPFDLKSVPLATTPMAEQRPESTATAAVKQPEKVAATRQEIFQEQLAAVPEFQGLGPLFKSSPEPVALT ESETEYVIRCTKHTFSDHLVFQFDCTNTLNDQTLENVTVQMEPTEAYEVLSYVPARSLPYNQPGTCYTLVALPTEDPTAV ACTFSCVMKFTVKDCDPNTGEIDEEGYEDEYVLEDLEVTVADHIQKVMKVNFEAAWDEVGDEFEKEETFTLSTIKTLEEA VGNIVKFLGMHPCERSDKVPENKNTHTLLLAGVFRGGHDILVRSRLLLLDTVTMQVTARSSEELPVDIILASVG Q9QZE5 Coatomer subunit zeta-1 Mus musculus 0.020218168 2 Spodoptera frugiperda LEVO MEALILEPSLYTVKAILILDNDGDRLFAKYYDDTYPSVKEQKAFEKNIFNKTHRTDSEIALLEGLTVVYKSSIDLYFYVI GSSYENELMLMAVLNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIVDGGVILESDPQQVVHRVALRGEDVPLTEQTV SQVLQSAKEQIKWSLLR P61924 ADP-ribosylation factor GTPase-activating protein 2 Rattus norvegicus 0.056629245999999994 1 Spodoptera frugiperda LEVO MAAGPSKSEIQTLFKRLRAIPTNKACFDCGAKSPSWASITYGVFLCIDCSGVHRSLGVHLSFIRSTELDSNWSWLQLRCM QVGGNANATAFFRQHGCLANDANTKYNSRAAQMYREKIRQLGSTALARHGTDLWIDNMNSAPSHSPEKKDSDFFTEHTQA PAWDTAATDPSGTQQPALPSESSSLAQPEPGPNTDLLGTSPQASLELKSSIIGKKKPAAAKKGLGAKKGLGAQKVSNQSF TEIERQAQVAEKLREQQAADAKKQAEESMVASMRLAYQELQIDRKKEEKKLQNLEGKKREQAERLGMGLVSRSSISHSVL SEMQMIEQETPLSAKSSRSQLDLFDDVGTFASGPPKYKDNPFSLGETFGSRWDSDAAWGMDRVEEKEPEVTISSIRPISE RTTSRREVESRISGLESSEARQKFAGAKAISSDMFFGREVDSEYEARSRLQQLSGSSAISSSDLFGDVDGAHGGGTVSLG NVLPTADIAQFKQGVKSVAGKMAVLANGVMNSLQDRYGSY Q3MID3 subtomogramAveraging threeDArray 7.4 50.0 HEPES 50.0 KOAc 1.0 MgCl2

Protein-A conjugated 10 nm gold was added to the reaction mix in 1:6 volume ratio before plunge-freezing

C-flat COPPER 200 CARBON HOLEY GLOW DISCHARGE 30 AIR

Protochips C-flat MultiHole, 20 mA

ETHANE 85 296 HOMEMADE PLUNGER

The sample was applied onto glow-discharged (30 sec, 20 mA) C-flat (Protochips Inc.) multihole grids. The grids were blotted from the back side for 11 seconds at room temperature in a chamber at 85% humidity and plunge-frozen into liquid ethane using a manual plunger..

COPI-coated vesicles were produced in vitro by incubating coatomer, Arf1, GTPgS, ARNO and GUVs in a total volume of 40 ul for 30 minutes at 37C

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 2.5 5.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS 0 20

Tomographic tilt series were acquired with the dose-symmetric tilt-scheme (Hagen et al., J Struct Biol. 2017)

GATAN K2 QUANTUM (4k x 4k) SUPER-RESOLUTION 1-5 1 2.0

Each of the images in the tilt series was low-pass filtered according to the electron-dose acquired by the sample (Grant and Grigorieff, 2015).

1 1 C1 10.1 FSC 0.143 CUT-OFF TOM Toolbox AV3

After classification and multi-reference alignment, the final COPI-ArfGAP2 class contained 12372 asymmetric units, comprising in total approximately 65 % of the initial dataset.

12372 27 105663 EMDB-2985 low pass filtered to 55A Amira TOM Toolbox

The dataset consisted of 27 tomograms containing 690 vesicles and near-complete buds. Subtomograms were extracted from the surface of the vesicles.

2 12000.0 TOM Toolbox AV3

Multireference alignment and classification on the complete leaf structure was performed in order to identify the subpopulation of leaves with bound ArfGAP2. To do this, the subtomograms were aligned against the reference from the COPI-ArfGAP2-dataset and from the COPI-dataset and divided into two classes based on cross-correlation. The average structures were generated for both classes.

NOT APPLICABLE emd_3721.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 227.84 227.84 227.84 90.0 90.0 90.0 X Y Z -0.19006988 0.22196983 0.0003264124 0.025159746 1.78 1.78 1.78 0.03 AUTHOR ::::EMDATABANK.org::::EMD-3721:::: The structure of the COPI coat leaf in complex with ArfGAP2 uncoating factor FLEXIBLE FIT Cross-correlation coefficient REAL