2025-10-22 REL PDBe INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-03-28 2025-10-22 2025-10-22 2025-10-22 Max Planck Society Germany Medical Research Council (MRC, United Kingdom) MC_U105178783 United Kingdom Medical Research Council (MRC, United Kingdom) MC_UP_1201/16 United Kingdom Wellcome Trust 227915/Z/23/Z United Kingdom European Molecular Biology Organization (EMBO) ALTF-383-2022 European Union The structure of the COPI leaf bound to GOLPH3 Taylor RJ Tagiltsev G Ciazynska KA Briggs JAG COPI coated vesicles, GOLPH3, Golgi transport, vesicular transport, STRUCTURAL PROTEIN Taylor RJ Zubkov N Ciazynska KA Kaufman JGG Tagiltsev G Owen DJ Briggs JAG Munro S The mechanistic basis of cargo selection during Golgi maturation. Sci Adv US 11 eaea0016 eaea0016 2025 41042862 doi:10.1126/sciadv.aea0016 2375-2548 9qpq FULLOVERLAP EMDB EMD-53278 associated EM volume
The structure of the COPI leaf bound to GOLPH3
 Reconstitution of COPI-coated vesicles containing the cargo adaptor protein GOLPH3 Reconstitution of COPI-coated vesicles containing the cargo adaptor protein GOLPH3 0 1 2 3 4 5 6 7 8 Mus musculus Mus musculus COPI coatomer complex, recombinantly expressed in insect cells and purified 1 2 3 4 5 6 7 Mus musculus Homo sapiens GOLPH3, recombinantly expressed in E. coli and purified 1 1 Homo sapiens Homo sapiens Arf1, recombinantly expressed in E. coli and purified 1 8 Homo sapiens Golgi phosphoprotein 3 Homo sapiens 0.033859555 2 Escherichia coli LEVO MTSLTQRSSGLVQRRTEASRNAADKERAAGGGAGSSEDDAQSRRDEQDDDDKGDSKETRLTLMEEVLLLGLKDREGYTSF WNDCISSGLRGCMLIELALRGRLQLEACGMRRKSLLTRKVICKSDAPTGDVLLDEALKHVKETQPPETVQNWIELLSGET WNPLKLHYQLRNVRERLAKNLVEKGVLTTEKQNFLLFDMTTHPLTNNNIKQRLIKKVQEAVLDKWVNDPHRMDRRLLALI YLAHASDVLENAFAPLLDEQYDLATKRVRQLLDLDPEVECLKANTNEVLWAVVAAFTK Q9H4A6 Coatomer subunit alpha Mus musculus 0.138617672 2 Trichoplusia ni LEVO MLTKFETKSARVKGLSFHPKRPWILTSLHNGVIQLWDYRMCTLIDKFDEHDGPVRGIDFHKQQPLFVSGGDDYKIKVWNY KLRRCLFTLLGHLDYIRTTFFHHEYPWILSASDDQTIRVWNWQSRTCVCVLTGHNHYVMCAQFHPSEDLVVSASLDQTVR VWDISGLRKKNLSPGAVESDVRGITGVDLFGTTDAVVKHVLEGHDRGVNWAAFHPTMPLIVSGADDRQVKIWRMNESKAW EVDTCRGHYNNVSCAVFHPRQELILSNSEDKSIRVWDMSKRTGVQTFRRDHDRFWVLAAHPNLNLFAAGHDGGMIVFKLE RERPAYAVHGNMLHYVKDRFLRQLDFNSSKDVAVMQLRSGSKFPVFNMSYNPAENAVLLCTRASNLENSTYDLYTIPKDA DSQNPDAPEGKRSSGLTAVWVARNRFAVLDRMHSLLIKNLKNEITKKIQVPNCDEIFYAGTGNLLLRDADSITLFDVQQK RTLASVKISKVKYVIWSADMSHVALLAKHAIVICNRKLDALCNIHENIRVKSGAWDESGVFIYTTSNHIKYAVTTGDHGI IRTLDLPIYVTRVKGNNVYCLDRECRPRVLTIDPTEFKFKLALINRKYDEVLHMVRNAKLVGQSIIAYLQKKGYPEVALH FVKDEKTRFSLALECGNIEIALEAAKALDDKNCWEKLGEVALLQGNHQIVEMCYQRTKNFDKLSFLYLITGNLEKLRKMM KIAEIRKDMSGHYQNALYLGDVSERVRILKNCGQKSLAYLSAATHGLDEEAESLKETFDPEKETIPDIDPNAKLLQPPAP IMPLDTNWPLLTVSKGFFEGSIASKGKGGALAADIDIDTVGTEGWGEDAELQLDEDGFVEAPEGLGEDVLGKGQEEGGGW DVEEDLELPPELDVPSGVSGSAEDGFFVPPTKGTSPTQIWCNNSQLPVDHILAGSFETAMRLLHDQVGVIQFGPYKQLFL QTYARGRTTYQALPCLPSMYSYPNRNWKDAGLKNGVPAVGLKLNDLIQRLQLCYQLTTVGKFEEAVEKFRSILLSVPLLV VDNKQEIAEAQQLITICREYIVGLCMEIERKKLPKETLDQQKRICEMAAYFTHSNLQPVHMILVLRTALNLFFKLKNFKT AATFARRLLELGPKPEVAQQTRKILSACEKNPTDACQLNYDMHNPFDICAASYRPIYRGKPVEKCPLSGACYSPEFKGQI CRVTTVTEIGKDVIGLRISPLQFR Q8CIE6 Coatomer subunit beta' Mus musculus 0.10256607799999999 2 Trichoplusia ni LEVO MPLRLDIKRKLTARSDRVKSVDLHPTEPWMLASLYNGSVCVWNHETQTLVKTFEVCDLPVRAAKFVARKNWVVTGADDMQ IRVFNYNTLERVHMFEAHSDYIRCIAVHPTQPFILTSSDDMLIKLWDWDKKWSCSQVFEGHTHYVMQIVINPKDNNQFAS ASLDRTIKVWQLGSSSPNFTLEGHEKGVNCIDYYSGGDKPYLISGADDRLVKIWDYQNKTCVQTLEGHAQNVSCASFHPE LPIIITGSEDGTVRIWHSSTYRLESTLNYGMERVWCVASLRGSNNVALGYDEGSIIVKLGREEPAMSMDANGKIIWAKHS EVQQANLKAMGDTEIKDGERLPLAVKDMGSCEIYPQTIQHNPNGRFVVVCGDGEYIIYTAMALRNKSFGSAQEFAWAHDS SEYAIRESNSIVKIFKNFKEKKSFKPDFGAESIYGGFLLGVRSVNGLAFYDWENTELIRRIEIQPKHIFWSDSGELVCIA TEESFFILKYLSEKVLAAQETHEGVTEDGIEDAFEVLGEIQEIVKTGLWVGDCFIYTSSVNRLNYYVGGEIVTIAHLDRT MYLLGYIPKDNRLYLGDKELNIVSYSLLVSVLEYQTAVMRRDFSMADKVLPTIPKEQRTRVAHFLEKQGFKQQALTVSTD PEHRFELALQLGELKIAYQLAVEAESEQKWKQLAELAISKCQFSLAQECLHHAQDYGGLLLLATASGNASMVNKLAEGAE RDGKNNVAFMSYFLQGKLDACLELLIRTGRLPEAAFLARTYLPSQVSRVVKLWRENLSKVNQKAAESLADPTEYENLFPG LKEAFVVEEWVKETHADLWPAKQYPLVTPNEERNVMEEAKGFQPSRPTAQQEPDGKPASSPVIMASQTTHKEEKSLLELE VDLDNLELEDIDTTDINLDEDILDD O55029 Coatomer subunit beta Mus musculus 0.107197961 4 Trichoplusia ni LEVO MTAAENVCYTLINVPMDSEPPSEISLKNDLEKGDVKSKTEALKKVIIMILNGEKLPGLLMTIIRFVLPLQDHTIKKLLLV FWEIVPKTTPDGRLLHEMILVCDAYRKDLQHPNEFIRGSTLRFLCKLKEAELLEPLMPAIRACLEHRHSYVRRNAVLAIY TIYRNFEHLIPDAPELIHDFLVNEKDASCKRNAFMMLIHADQDRALDYLSTCIDQVQTFGDILQLVIVELIYKVCHANPS ERARFIRCIYNLLQSSSPAVKYEAAGTLVTLSSAPTAIKAAAQCYIDLIIKESDNNVKLIVLDRLVELKEHPAHERVLQD LVMDILRVLSTPDLEVRKKTLQLALDLVSSRNVEELVIVLKKEVIKTNNVSEHEDTDKYRQLLVRTLHSCSVRFPDMAAN VIPVLMEFLSDSNEAAAADVLEFVREAIQRFDNLRMLIVEKMLEVFHAIKSVKIYRGALWILGEYCSTKEDIQSVMTEVR RSLGEIPIVESEIKKEAGELKPEEEITVGPVQKLVTEMGTYATQSALSSSRPTKKEEDRPPLRGFLLDGDFFVAASLATT LTKIALRYVALVQEKKKQNSFVAEAMLLMATILHLGKSSLPKKPITDDDVDRISLCLKVLSECSPLMNDIFNKECRQSLS QMLSAKLEEEKLSQKKESEKRNVTVQPDDPISFMQLTAKNEMNCKEDQFQLSLLAAMGNTQRKEAADPLASKLNKVTQLT GFSDPVYAEAYVHVNQYDIVLDVLVVNQTSDTLQNCTLELATLGDLKLVEKPSPLTLAPHDFANIKANVKVASTENGIIF GNIVYDVSGAASDRNCVVLSDIHIDIMDYIQPATCTDAEFRQMWAEFEWENKVTVNTNMTDLNDYLQHILKSTNMKCLTP EKALSGYCGFMAANLYARSIFGEDALANVSIEKPVHQGPDAAVTGHIRIRAKSQGMALSLGDKINLSQKKTSL Q9JIF7 Coatomer subunit delta Mus musculus 0.057304249999999994 1 Trichoplusia ni LEVO MVLLAAAVCTKAGKAIVSRQFVEMTRTRIEGLLAAFPKLMNTGKQHTFVETESVRYVYQPMEKLYMVLITTKNSNILEDL ETLRLFSRVIPEYCRALEENEISEHCFDLIFAFDEIVALGYRENVNLAQIRTFTEMDSHEEKVFRAVRETQEREAKAEMR RKAKELQQARRDAERQGKKAPGFGGFGSSAVSGGSTAAMITETIIETDKPKVAPAPARPSGPSKALKLGAKGKEVDNFVD KLKSEGETIMSSNMGKRTSEATKVHAPPINMESVHMKIEEKITLTCGRDGGLQNMELHGMIMLRISDDKFGRIRLHVENE DKKGVQLQTHPNVDKKLFTAESLIGLKNPEKSFPVNSDVGVLKWRLQTTEESFIPLTINCWPSESGNGCDVNIEYELQED NLELNDVVITIPLPSGVGAPVIGEIDGEYRHDSRRNTLEWCLPVIDAKNKSGSLEFSIPGQPNDFFPVQVSFISKKNYCN IQVTKVTQVDGNSPVRFSTETTFLVDKYEIL Q5XJY5 Coatomer subunit gamma-1 Mus musculus 0.09762270299999999 3 Trichoplusia ni LEVO MLKKFDKKDEESGGGSNPLQHLEKSAVLQEARVFNETPINPRKCAHILTKILYLINQGEHLGTTEATEAFFAMTKLFQSN DPTLRRMCYLTIKEMSCIAEDVIIVTSSLTKDMTGKEDNYRGPAVRALCQITDSTMLQAVERYMKQAIVDKVPSVSSSAL VSSLHLLKCSFDVVKRWVNEAQEAASSDNIMVQYHALGLLYHVRKNDRLAVSKMISKFTRHGLKSPFAYCMMIRVASKQL EEEDGSRDSPLFDFIESCLRNKHEMVVYEAASAIVNLPGCSAKELAPAVSVLQLFCSSPKAALRYAAVRTLNKVAMKHPS AVTACNLDLENLVTDSNRSIATLAITTLLKTGSESSIDRLMKQISSFMSEISDEFKVVVVQAISALCQKYPRKHAVLMNF LFTMLREEGGFEYKRAIVDCIISIIEENSESKETGLSHLCEFIEDCEFTVLATRILHLLGQEGPKTNNPSKYIRFIYNRV VLEHEEVRAGAVSALAKFGAQNEEMLPSILVLLKRCVMDDDNEVRDRATFYLNVLEQKQKALNAGYILNGLTVSIPGLEK ALQQYTLEPSEKPFDLKSVPLATTPMAEQRPESTATAAVKQPEKVAATRQEIFQEQLAAVPEFQGLGPLFKSSPEPVALT ESETEYVIRCTKHTFSDHLVFQFDCTNTLNDQTLENVTVQMEPTEAYEVLSYVPARSLPYNQPGTCYTLVALPTEDPTAV ACTFSCVMKFTVKDCDPNTGEIDEEGYEDEYVLEDLEVTVADHIQKVMKVNFEAAWDEVGDEFEKEETFTLSTIKTLEEA VGNIVKFLGMHPCERSDKVPENKNTHTLLLAGVFRGGHDILVRSRLLLLDTVTMQVTARSSEELPVDIILASVG Q9QZE5 Coatomer subunit zeta-1 Mus musculus 0.020218168 1 Trichoplusia ni LEVO MEALILEPSLYTVKAILILDNDGDRLFAKYYDDTYPSVKEQKAFEKNIFNKTHRTDSEIALLEGLTVVYKSSIDLYFYVI GSSYENELMLMAVLNCLFDSLSQMLRKNVEKRALLENMEGLFLAVDEIVDGGVILESDPQQVVHRVALRGEDVPLTEQTV SQVLQSAKEQIKWSLLR P61924 ADP-ribosylation factor 1 Homo sapiens 0.020721741999999998 3 Escherichia coli LEVO MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRH YFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCA TSGDGLYEGLDWLSNQLRNQK P84077 3.6.5.2 subtomogramAveraging particle 7.2 50.0 HEPES HEPES 125.0 KAc Potassium acetate 2.5 MgCl2 Magnesium chloride C-flat-2/2 COPPER 300 CARBON HOLEY 50.0 GLOW DISCHARGE AIR ETHANE-PROPANE 100 293 LEICA EM CPC
Budded and budding COPI vesicles were reconstituted by mixing liposomes with purified COPI coat protein, Arf1, GTPgammaS, and GOLPH3.
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.5 3.5 53000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 BIOQUANTUM (6k x 4k) 1 3.114 1 C1 7.5 FSC 0.143 CUT-OFF RELION v3.0 108432 206 193104 EMDB-2985 subTOM v1.1.5 https://github.com/DustinMorado/subTOM
A total of 4866 COPI vesicles and buds were manually picked from 206 tomograms in UCSF Chimera. The center of each coated vesicle or bud was picked and radii were assigned using a custom-written plugin (https://www.biochem.mpg.de/7940000/Pick-Particle). Initial coordinates for subsequent particle search were seeded with an even spacing of 10.9 nm (8 pixels in tomograms binned 8 times) perpendicular to the sphere surface, and with random in-plane rotation, yielding a total of 193104 particles (C3).
 NOVACTF PHASE FLIPPING AND AMPLITUDE CORRECTION MAXIMUM LIKELIHOOD RELION v3.0 emd_53278.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 292 292 292 0 0 0 292 292 292 499.32 499.32 499.32 90.0 90.0 90.0 X Y Z -0.023333697 0.042098027 0.00029214047 0.0015516926 1.71 1.71 1.71 0.0053 AUTHOR COPI heptameric leaf bound to GOLPH3 on membranes Q8CIE6 1-824 AlphaFold in silico model O55029 1-838 AlphaFold in silico model Q9JIF7 1-710 AlphaFold in silico model
1-499; 536-710
 Q5XJ75 1-247 AlphaFold in silico model
1-177; 224-247
 Q9QZE5 1-582 AlphaFold in silico model P61924 6-150 AlphaFold in silico model P84077 15-181 AlphaFold in silico model Q9H4A6 10-290 AlphaFold in silico model
10-25; 55-298
 RIGID BODY FIT 200.0 emd_53278_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 292 292 292 0 0 0 292 292 292 499.32 499.32 499.32 90.0 90.0 90.0 X Y Z -0.01579778 0.01912006 0.00014834058 0.0017265324 1.71 1.71 1.71 AUTHOR COPI heptameric leaf bound to GOLPH3 on membranes emd_53278_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 292 292 292 0 0 0 292 292 292 499.32 499.32 499.32 90.0 90.0 90.0 X Y Z -0.01315367 0.019166958 0.00014381066 0.0017073386 1.71 1.71 1.71 AUTHOR COPI heptameric leaf bound to GOLPH3 on membranes