AP2 in clathrin coats assembled on a membrane containing dileucine- and tyrosine-based cargo peptides

2024-05-22 REL PDBe PDBe PDBe 2020-03-12 2020-07-29 2020-07-29 2024-05-22 Wellcome Trust 207455/Z/17/Z United Kingdom Medical Research Council (MRC, United Kingdom) MC_UP_1201/16 United Kingdom AP2 in clathrin coats assembled on a membrane containing dileucine- and tyrosine-based cargo peptides Kovtun O Kane Dickson V clathrin, clathrin adaptor, ap2, clathrin assembly, ENDOCYTOSIS Kovtun O Dickson VK Kelly BT Owen DJ Briggs JAG Architecture of the AP2/clathrin coat on the membranes of clathrin-coated vesicles. Sci Adv US 6 eaba8381 eaba8381 2020 32743075 doi:10.1126/sciadv.aba8381 2375-2548 EMD-10747 other EM volume

AP2 core in physiological buffer

EMD-10748 other EM volume EMD-10749 other EM volume EMD-10750 other EM volume EMD-10752 other EM volume EMD-10753 other EM volume EMD-10754 other EM volume 6yah FULLOVERLAP Clathrin/AP2 coat assembled on AP2 membrane. Clathrin/AP2 coat assembled on AP2 membrane. 0 1 2 3 4

Clathrin/AP coat was formed on the membrane containing dileucine- and tyrosine-based cargo signal peptides. The AP2 adaptor lacked hinge and appendage regions in its alpha subunit.

AP-2 complex in clathrin coat, subunits alpha-2 and mu 1 1 3

AP2 in clathrin coat formed on membranes containing dileucine- and tyrosine-based cargo peptides

Rattus norvegicus AP-2 complex in clathrin coat, subunit beta 1 2

AP2 in clathrin coat formed on membranes containing dileucine- and tyrosine-based cargo peptides

Homo sapiens AP-2 complex in clathrin coat, subunit sigma 1 4

AP2 in clathrin coat formed on membranes containing dileucine- and tyrosine-based cargo peptides

Mus musculus AP-2 complex subunit alpha-2 Rattus norvegicus 0.070310062 1 Escherichia coli LEVO MPAVSKGDGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVCKLLFIFLLGHDIDFGHMEAV NLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDLASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDT MDSVKQSAALCLLRLYRTSPDLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA STDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKVQHSNAKNAVLFEAISLIIHH DSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSEFSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRS NAQQIVAEMLSYLETADYSIREEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAA KTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRALLLSTYIKFVNLFPEVKATIQ DVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLEEMPPFPERESSILAKLKKKKGGSGLVPR P18484 AP-2 complex subunit beta Homo sapiens 0.10561934399999999 1 Escherichia coli LEVO MHHHHHHMTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVYLYL MNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINA QMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKD DREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKR PEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVS TLLDLIQTKVNYVVQEAIVVIRDIFRKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGF HDESTQVQLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETD LIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLLGDLLN LDLGPPVNVPQVSSMQMGAVDLLGGGLDSLVGQSFIPSSVPATFAPSPTPAVVSSGLNDLFELSTGIGMAPGGYVAPKAV WLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAIHTPLMPNQSIDVSLPLNTLGP VMKMEPLNNLQVAVKNNIDVFYFSCLIPLNVLFVEDGKMERQVFLATWKDIPNENELQFQIKECHLNADTVSSKLQNNNV YTIAKRNVEGQDMLYQSLKLTNGIWILAELRIQPGNPNYTLSLKCRAPEVSQYIYQVYDSILKN P63010 AP-2 complex subunit mu Rattus norvegicus 0.051044112999999995 1 Escherichia coli LEVO MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKRSNIWLAAVTKQNVNAAMVFE FLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYPQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIG WRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSMEQK LISEEDLGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKLEVKVVIKS NFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMN FEVPFAPSGLKVRYLKVFEPKLNYSDHDVIKWVRYIGRSGIYETRC P84092 AP-2 complex subunit sigma Mus musculus 0.017038687999999996 1 Escherichia coli LEVO MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAY LEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE P62743 subtomogramAveraging threeDArray 0.7 7.2 10.0 Hepes KOH 120.0 Potassium Acetate 2.0 Magnesium chloride 5.0 2-Mercaptoethanol C-flat-2/2 CARBON HOLEY ETHANE 98 291 LEICA EM GP

The sample was supplemented with 10 nm nanogold fiducials, and 3 ul of the mixture was backside blotted for 3 seconds..

The sample (in vitro budding reaction) contained AP2, clathrin and 400 nm extruded liposomes

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.5 1.5 6.5 6.5 81000.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS 20 GATAN K2 QUANTUM (4k x 4k) COUNTING 3838 3710 1-10 2 0.2 3.2

The images were collected in movie mode at 10 frames per second

The images were low pass filtered according to the cumulative radiation dose.

C1 10.2 FSC 0.143 CUT-OFF TOM AV3 27630 29139 292224 reference-free geometrically defined initial positions on membrane strctures PEET Dynamo OTHER TOM AV3 emd_10751.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 120 120 120 0 0 0 120 120 120 214.43999 214.43999 214.43999 90.0 90.0 90.0 X Y Z -2.3564742 2.5479515 -0.00039217158 0.21370192 1.787 1.787 1.787 0.3 AUTHOR ::::EMDATABANK.org::::EMD-10751:::: Sharpened map of AP2 in clathrin coat formed on membranes containing dileucine- and tyrosine-based cargo peptides 1XA7 PDB experimental model FLEXIBLE FIT correlation coefficient REAL emd_10751_msk_1.map emd_10751_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 120 120 120 0 0 0 120 120 120 214.43999 214.43999 214.43999 90.0 90.0 90.0 X Y Z -1.0087405 1.1976513 0.0018526256 0.14044191 1.787 1.787 1.787 AUTHOR ::::EMDATABANK.org::::EMD-10751:::: Unsharpened half-map of AP2 in clathrin coat formed on membranes containing dileucine- and tyrosine-based cargo peptides emd_10751_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 120 120 120 0 0 0 120 120 120 214.43999 214.43999 214.43999 90.0 90.0 90.0 X Y Z -0.97267383 1.0434717 0.0018831847 0.122059956 1.787 1.787 1.787 AUTHOR ::::EMDATABANK.org::::EMD-10751:::: Unsharpened half-map of AP2 in clathrin coat formed on membranes containing dileucine- and tyrosine-based cargo peptides