Mammalian AP3 complex on tubular membranes (AP3 centered)

2026-05-27 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-07-03 2026-05-27 2026-05-27 2026-05-27 Wellcome Trust 227915/Z/23/Z United Kingdom Wellcome Trust 207455/Z/17/Z United Kingdom Max Planck Society Germany Medical Research Council (MRC, United Kingdom) MC_UP_1201/16 United Kingdom Medical Research Council (MRC, United Kingdom) MR/N013433/1 United Kingdom European Molecular Biology Organization (EMBO) ALTF-383-2022 European Union Biotechnology and Biological Sciences Research Council (BBSRC) BB/W005905/ United Kingdom UK Research and Innovation (UKRI) UKRI715 United Kingdom Wellcome Trust 210481 United Kingdom Mammalian AP3 complex on tubular membranes (AP3 centered) Kaufman JGG Tagiltsev G Briggs JAG Owen DJ Cargo adapter, Coat, trafficking, ENDOCYTOSIS Kaufman JGG Tagiltsev G Stalder DS Taylor RJ Sava I Guo H Ciazynska KA Zaccai NR Gray SR Vallis Y Honing S Kelly BT Gershlick DC Briggs JAG Owen DJ Architecture of clathrin-independent AP3:ARF1-coated carriers. Sci Adv US 12 eaed1529 eaed1529 2026 42139345 doi:10.1126/sciadv.aed1529 2375-2548 9rtw FULLOVERLAP EMDB EMD-54255 associated EM volume

Mammalian AP-3 complex assembled on tubular membranes Mammalian AP-3 complex assembled on tubular membranes 0 1 2 3 4 5

helical

Homo sapiens 1592.786 AP-3 complex subunit beta Pan troglodytes 0.06395698799999999 1 Spodoptera frugiperda LEVO KNEDLKQMLESNKDSAKLDAMKRIVGMIAKGKNASELFPAVVKNVASKNIEIKKLVYVYLVRYAEEQQDLALLSISTFQR ALKDPNQLIRASALRVLSSIRVPIIVPIMMLAIKEASADLSPYVRKNAAHAIQKLYSLDPEQKEMLIEVIEKLLKDKSTL VAGSVVMAFEEVCPDRIDLIHKNYRKLCNLLVDVEEWGQVVIIHMLTRYARTQFVSPWTMDPDHRLLIRNTKPLLQSRNA AVVMAVAQLYWHISPKSEAGIISKSLVRLLRSNREVQYIVLQNIATMSIQRKGMFEPYLKSFYVRSTDPTMIKTLKLEIL TNLANEANISTLLREFQTYVKSQDKQFAAATIQTIGRCATNILEVTDTCLNGLVCLLSNRDEIVVAESVVVIKKLLQMQP AQHGEIIKHMAKLLDSITVPVARASILWLIGENCERVPKIAPDVLRKMAKSFTSEDDLVKLQILNLGAKLYLTNSKQTKL LTQYILNLGKYDQNYDIRDRTRFIRQLIVPNEKSGALSKYAKKIFLAQKPAPLLESPFKDRDHFQLGTLSHTLNIKATGY LEL A0A2I3SW12 AP-3 complex subunit delta-1 Homo sapiens 0.06906133599999999 1 Spodoptera frugiperda LEVO LQDLVRGIRNHKEDEAKYISQCIDEIKQELKQDNIAVKANAVCKLTYLQMLGYDISWAAFNIIEVMSASKFTFKRIGYLA ASQSFHEGTNVIMLTTNQIRKDLSSPSQYDTGVALTGLSCFVTPDLARDLANDIMTLMSHTKPYIRKKAVLIMYKVFLKY PESLRPAFPRLKEKLEDPDPGVQSAAVNVICELARRNPKNYLSLAPLFFKLMTSSTNNWVLIKIIKLFGALTPLEPRLGK KLIEPLTNLIHSTSAMSLLYECVNTVIAVLISLSSGMPNHSASIQLCVQKLRILIEDSDQNLKYLGLLAMSKILKTHPKS VQSHKDLILQCLDDKDESIRLRALDLLYGMVSKKNLMEIVKKLMTHVDKAEGTTYRDELLTKIIDICSQSNYQYITNFEW YISILVELTRLEGTRHGHLIAAQMLDVAIRVKAIRKFAVSQMSALLDSAHLLASSTQRNGICEVLYAAAWICGEFSEHLQ EPHHTLEAMLRPRVTTLPGHIQAVYVQNVVKLYASILQQKEQAGEAEGAQAVTQLMVDRLPQFVQSADLEVQERASCILQ LVKHIQKLQAKDVPVAEEVSALFAGELNPVAPKAQKKVPVPEGLDLDAWINEPLS O14617 ADP-ribosylation factor 1 Homo sapiens 0.01920993 4 Escherichia coli BL21(DE3) LEVO KKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDS NDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLS NQLRNQK P84077 3.6.5.2 AP-3 complex subunit mu-1 Rattus norvegicus 0.04701798 1 Spodoptera frugiperda LEVO MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIYRDKLFFVSVIQTEVSPLFVI EFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPLATESNILKELIKPPTILRSVVNSITGSSNVGDTLPTG QLSNIPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDLSLSFMNPRLLDDVSFHPCIRFK RWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHNISFKENSSCGRFDITIGPKQNMGKTIEGITVTVHMPKVVLN MNLTPTQGSYTFDPVTKVLAWDVGKITPQKLPSLKGLVNLQSGAPKPEENPNLNIQFKIQQLAISGLKVNRLDMYGEKYK PFKGVKYITKAGKFQVRT A6KKR5 AP-3 complex subunit sigma-1 Homo sapiens 0.017566105 1 Spodoptera frugiperda LEVO MIKAILIFNNYGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSDNKLIYRHYATLYFVFCVDSS ESELGILDLIQVFVETLDKCFENVCELDLIFHVDKVHNILAEMVMGGMVLETNMNEIVTQIDAQNKLEKSEAG Q92572 subtomogramAveraging helicalArray 7.4 200.0 NaCl sodium chloride 20.0 Tris-HCl Tris(hydroxymethyl)aminomethane-HCl 1.0 TCEP Tris(2-carboxyethyl)phosphine C-flat-2/2 COPPER CARBON HOLEY GLOW DISCHARGE 90 ETHANE-PROPANE 100 284 FEI VITROBOT MARK IV

Purified recombinant AP3 complex was reconstituted with mystoylated ARF1 GTPase on GUV containing lipidated cargo motif sequences (TGN38:CKVTRRPKASDYQRL and MFSD12:GEHTPLLAPATC). Reconstituted AP3 spontaneously assembled to tubulate membranes.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 3.0 6.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X TFS FALCON 4i (4k x 4k) 1 3.0 1 C1 7.4 FSC 0.143 CUT-OFF RELION 42469 32 121939 reference free STA UCSF Chimera subTOM Warp M RELION Warp

3DCTF in WARP

PHASE FLIPPING AND AMPLITUDE CORRECTION RELION MAXIMUM LIKELIHOOD RELION emd_54255.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 182 182 182 0 0 0 182 182 182 400.4 400.4 400.4 90.0 90.0 90.0 X Y Z -0.007814548 0.01318146 0.00005880319 0.0005775094 2.2 2.2 2.2 0.002 AUTHOR ::::EMDATABANK.org::::EMD-54255:::: AlphaFold in silico model RIGID BODY FIT

Alphafold 3 (AF3), was used to generate 5 models of mammalian AP3 in complex with two copies of ARF1 in the GTP bound conformation. As the structure from STA was in a much more extended conformation than AF3 models or previous structures, direct rigid body docking of the complete AF3 model into the STA density was not possible. To create the C1 model the predicted complex was separated into three submodels, each of which was independently fitted into the map as a rigid body. Submodel 1 consisted of sigma3 (1-193), delta (1-387), delta-ARF1 (1-181). Submodel 2 consisted of mu3 (1-418), beta3 (1-472), beta3-ARF1. Submodel 3 consisted of beta3 (473-636) and delta (388-638) formed submodel 3. Rigid body fitting was performed using ChimeraX. This positioned truncated regions of submodels 1 and 2 in close proximity to their adjoining regions in submodel3, thus the split beta3 and delta chains were rejoined into single chains before real-space refinement in COOT to correct bond angles, distances and torsions. Using the previously resolved ARF1 dimer (PDBID: 9C5A), ARF1 was first superimposed with the existing ARF1 on beta3 and delta before rigid docking into the EM density. Flexible regions not accounted for sufficiently by modellable density were removed, these regions are listed as follows; beta3 (1-42), beta3 (259-292), delta (1-17), sigma3 (154-193) and ARF1 (1-13). Side chains and rotamers were not modelled and were therefore removed in ChimeraX.

REAL emd_54255_msk_1.map emd_54255_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 182 182 182 0 0 0 182 182 182 400.4 400.4 400.4 90.0 90.0 90.0 X Y Z -0.0068959924 0.012705969 0.00005813603 0.0007103554 2.2 2.2 2.2 AUTHOR ::::EMDATABANK.org::::EMD-54255:::: emd_54255_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 182 182 182 0 0 0 182 182 182 400.4 400.4 400.4 90.0 90.0 90.0 X Y Z -0.006709995 0.013387531 0.00005947035 0.0007135061 2.2 2.2 2.2 AUTHOR ::::EMDATABANK.org::::EMD-54255::::