9RTY: Mammalian AP3 complex on tubular membranes

Mammalian AP3 complex on tubular membranes (ARF1 centered Beta3-ARF1 dimer-Delta interface). Determined by electron microscopy at 8.9 Å resolution. Released 27 May 2026.

Method
Electron microscopy
Resolution
8.9 Å
Organisms
Pan troglodytes, Homo sapiens, Rattus norvegicus
Chains
14
Atoms
18,000
Mol. weight
682.35 kDa
Released
27 May 2026

Explore 9RTY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RTY contains 281 α-helices and 126 β-strands across 14 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain b: 46 helices, 1 β-strand

ElementResiduesLengthSheet
α-helix44-529
α-helix56-7116
α-helix77-793
α-helix80-845
α-helix85-884
α-helix92-10514
α-helix110-12314
α-helix129-14113
α-helix145-1473
α-helix148-15912
α-helix164-18017
α-helix182-1843
α-helix185-19612
α-helix201-21414
α-helix220-2234
α-helix226-2327
α-helix233-2353
α-helix238-25518
α-helix295-30410
α-helix305-3095
β-strand31011
α-helix313-32614
α-helix329-3324
α-helix335-3428
α-helix347-36317
α-helix365-3673
α-helix369-3757
α-helix376-3783
α-helix383-39614
α-helix402-41211
α-helix418-43417
α-helix436-4383
α-helix439-44911
α-helix455-47016
α-helix477-48610
α-helix493-50513
α-helix513-52412
α-helix525-5273
α-helix530-54617
α-helix548-56316
α-helix568-58114
α-helix589-5924
α-helix594-5996
α-helix603-6064
α-helix612-6143
α-helix6181
α-helix622-6265
Chain B: 47 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix44-529
α-helix56-7116
α-helix77-793
α-helix80-845
α-helix85-884
α-helix92-10514
α-helix110-12314
α-helix129-14113
α-helix145-1473
α-helix148-15912
α-helix164-18017
α-helix182-1843
α-helix185-19612
α-helix201-21414
α-helix219-2213
α-helix223-2253
α-helix226-2327
α-helix233-2353
α-helix238-25518
α-helix295-30410
α-helix305-3095
β-strand310115
α-helix313-32614
α-helix329-3324
α-helix335-3428
α-helix347-36317
α-helix365-3673
α-helix369-3757
α-helix376-3783
α-helix383-39614
α-helix402-41211
α-helix418-43417
α-helix436-4383
α-helix439-44911
α-helix455-47016
α-helix477-48610
α-helix493-50513
α-helix513-52412
α-helix525-5273
α-helix530-54617
α-helix548-56316
α-helix568-58114
α-helix589-5924
α-helix594-5996
α-helix603-6064
α-helix612-6143
α-helix6181
α-helix622-6265
Chains d and D: 45 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix19-279
α-helix32-4716
α-helix52-6716
α-helix73-753
α-helix76-838
α-helix88-10114
α-helix107-1115
α-helix112-1209
α-helix125-13814
α-helix141-15414
α-helix160-17617
α-helix178-1803
α-helix181-19010
α-helix191-1933
α-helix197-21317
α-helix215-2217
α-helix222-23110
α-helix235-24814
α-helix249-2513
α-helix253-26917
α-helix273-28917
α-helix297-31317
α-helix317-33115
α-helix335-3395
α-helix342-3487
α-helix354-36714
α-helix373-38513
α-helix389-40921
α-helix415-42511
α-helix434-44714
α-helix449-4513
α-helix452-46413
α-helix466-4694
α-helix480-49112
α-helix493-4953
α-helix499-5068
α-helix509-5135
α-helix516-53924
α-helix543-55614
α-helix558-5614
α-helix566-58621
α-helix593-5986
α-helix612-6143
α-helix615-6184
α-helix629-6313
Chains E, F, G, H, I and J: 8 helices, 9 β-strands
ElementResiduesLengthSheet
β-strand16-24916
α-helix30-389
β-strand43117
β-strand51-58816
β-strand61-68816
α-helix75-817
β-strand87-93716
α-helix97-993
α-helix100-11112
α-helix114-1163
β-strand120-126716
α-helix136-1438
α-helix145-1473
β-strand153-157516
β-strand159118
β-strand164118
α-helix166-17712
Chains m and M: 17 helices, 28 β-strands
ElementResiduesLengthSheet
β-strand2-987
β-strand14-1967
α-helix26-294
α-helix30-389
α-helix42-443
β-strand48-5037
β-strand55-6177
β-strand64-7077
α-helix76-9419
α-helix99-1046
α-helix106-11611
β-strand117-11828
β-strand121-12228
α-helix127-1337
β-strand13419
α-helix135-1373
α-helix139-14810
β-strand15319
α-helix159-1624
β-strand178-191141
β-strand197-211151
β-strand217-222610
α-helix225-2273
β-strand228-23361
β-strand237110
α-helix239-2457
β-strand248-250310
α-helix252-2532
β-strand255-264101
α-helix269-2713
β-strand274-282911
β-strand288-2971011
α-helix303-3042
β-strand305-31391
β-strand318-325811
β-strand329-33351
β-strand338-34471
β-strand347112
β-strand350112
β-strand353-360811
α-helix364-3674
α-helix370-3723
β-strand373-38081
β-strand389-395710
β-strand402-416151
Chains s and S: 8 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand2-9813
β-strand14-19613
α-helix25-4016
β-strand49-51313
α-helix52-532
α-helix54-563
α-helix58-603
β-strand61-68813
β-strand71-78813
α-helix83-10119
α-helix106-1116
α-helix113-12311
β-strand124-125214
β-strand128-129214
α-helix134-15219

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
AP-3 complex subunit betaB, bprotein658Pan troglodytesA0A2I3SW12 (AlphaFold model)
AP-3 complex subunit deltaD, dprotein1203Homo sapiensA0A8V8TQW4 (AlphaFold model)
ADP-ribosylation factor 1E, F, G, H, I, Jprotein181Homo sapiensP84077 (AlphaFold model)
AP-3 complex subunit mu-1M, mprotein418Rattus norvegicusA6KKR5 (AlphaFold model)
AP-3 complex subunit sigma-1S, sprotein193Homo sapiensQ92572
Sequence of entity 1 (B, b), FASTA
>9RTY_1 AP-3 complex subunit beta (chains B, b)
HHHHHHHHHHMASNSFPYNEQSGGGEATELGQEATSTISPSGAFGLFSSDLKKNEDLKQM
LESNKDSAKLDAMKRIVGMIAKGKNASELFPAVVKNVASKNIEIKKLVYVYLVRYAEEQQ
DLALLSISTFQRALKDPNQLIRASALRVLSSIRVPIIVPIMMLAIKEASADLSPYVRKNA
AHAIQKLYSLDPEQKEMLIEVIEKLLKDKSTLVAGSVVMAFEEVCPDRIDLIHKNYRKLC
NLLVDVEEWGQVVIIHMLTRYARTQFVSPWKEGDELEDNGKNFYESDDDQKEKTDKKKKP
YTMDPDHRLLIRNTKPLLQSRNAAVVMAVAQLYWHISPKSEAGIISKSLVRLLRSNREVQ
YIVLQNIATMSIQRKGMFEPYLKSFYVRSTDPTMIKTLKLEILTNLANEANISTLLREFQ
TYVKSQDKQFAAATIQTIGRCATNILEVTDTCLNGLVCLLSNRDEIVVAESVVVIKKLLQ
MQPAQHGEIIKHMAKLLDSITVPVARASILWLIGENCERVPKIAPDVLRKMAKSFTSEDD
LVKLQILNLGAKLYLTNSKQTKLLTQYILNLGKYDQNYDIRDRTRFIRQLIVPNEKSGAL
SKYAKKIFLAQKPAPLLESPFKDRDHFQLGTLSHTLNIKATGYLELSNWPEVAPDPSV
Sequence of entity 2 (D, d), FASTA
>9RTY_2 AP-3 complex subunit delta (chains D, d)
MALKMVKGSIDRMFDKNLQDLVRGIRNHKEDEAKYISQCIDEIKQELKQDNIAVKANAVC
KLTYLQMLGYDISWAAFNIIEVMSASKFTFKRIGYLAASQSFHEGTNVIMLTTNQIRKDL
SSPSQYDTGVALTGLSCFVTPDLARDLANDIMTLMSHTKPYIRKKAVLIMYKVFLKYPES
LRPAFPRLKEKLEDPDPGVQSAAVNVICELARRNPKNYLSLAPLFFKLMTSSTNNWVLIK
IIKLFGALTPLEPRLGKKLIEPLTNLIHSTSAMSLLYECVNTVIAVLISLSSGMPNHSAS
IQLCVQKLRILIEDSDQNLKYLGLLAMSKILKTHPKSVQSHKDLILQCLDDKDESIRLRA
LDLLYGMVSKKNLMEIVKKLMTHVDKAEGTTYRDELLTKIIDICSQSNYQYITNFEWYIS
ILVELTRLEGTRHGHLIAAQMLDVAIRVKAIRKFAVSQMSALLDSAHLLASSTQRNGICE
VLYAAAWICGEFSEHLQEPHHTLEAMLRPRVTTLPGHIQAVYVQNVVKLYASILQQKEQA
GEAEGAQAVTQLMVDRLPQFVQSADLEVQERASCILQLVKHIQKLQAKDVPVAEEVSALF
AGELNPVAPKAQKKVPVPEGLDLDAWINEPLSDSESEDERPRAVFHEEEQRRPKHRPSEA
DEEELARRREARKQEQANNPFYIKSSPSPQKRYQDTPGVEHIPVVQIDLSVPLKVPGLPM
SDQYVKLEEERRHRQKLEKDKRRKKRKEKEKKGKRRHSSLPTESDEDIAPAQQVDIVTEE
MPENALPSDEDDKDPNDPYRALDIDLDKPLADSEKLPIQKHRNTETSKSPEKDVPMVEKK
SKKPKKKEKKHKEKERDKEKKKEKEKKAEDLDFWLSTTPPPAPAPAPAPVPSTDECEDAK
TEAQGEEDDAEGQDQDKKSPKPKKKKHRKEKEERTKGKKKSKKQPPGSEEAAGEPVQNGA
PEEEQLPPESSYSLLAENSYVKMTCDIRGSLQEDSQVTVAIVLENRSSSILKGMELSVLD
SLNARMARPQGSSVHDGVPVPFQLPPGVSNEAQYVFTIQSIVMAQKLKGTLSFIAKNDEG
ATHEKLDFRLHFSCSSYLITTPCYSDAFAKLLESGDLSMSSIKVDGIRMSFQNLLAKICF
HHHFSVVERVDSCASMYSRSIQGHHVCLLVKKGENSVSVDGKCSDSTLLSNLLEEMKATL
AKC
Sequence of entity 3 (E, F, G, H, I, J), FASTA
>9RTY_3 ADP-ribosylation factor 1 (chains E, F, G, H, I, J)
MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKN
ISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAV
LLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQ
K
Sequence of entity 4 (M, m), FASTA
>9RTY_4 AP-3 complex subunit mu-1 (chains M, m)
MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIY
RDKLFFVSVIQTEVSPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNG
FPLATESNILKELIKPPTILRSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAY
FDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDLSLSFMNPRLLDDVSFHPCIRFK
RWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHNISFKENSSCGRFDITIGPKQN
MGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLAWDVGKITPQKLPSLKGLVNL
QSGAPKPEENPNLNIQFKIQQLAISGLKVNRLDMYGEKYKPFKGVKYITKAGKFQVRT
Sequence of entity 5 (S, s), FASTA
>9RTY_5 AP-3 complex subunit sigma-1 (chains S, s)
MIKAILIFNNYGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSD
NKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHVDKVHNIL
AEMVMGGMVLETNMNEIVTQIDAQNKLEKSEAGLAGAPARAVSAVKNMNLPEIPRNINIG
DISIKVPNLPSFK

Primary citation

Architecture of clathrin-independent AP3:ARF1-coated carriers. Kaufman, J.G.G., Tagiltsev, G., Stalder, D.S. et al. Sci Adv (2026) 12:eaed1529-eaed1529. DOI 10.1126/sciadv.aed1529 · PubMed

Other PDB entries of the same protein (UniProt A0A2I3SW12 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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