9C5C: AP-3 complex subunit delta-1

Structure of Human Adaptor Protein Complex AP-3 in the Apo State. Determined by electron microscopy at 3.6 Å resolution. Released 18 Dec 2024.

Method
Electron microscopy
Resolution
3.6 Å
Organism
Homo sapiens
Chains
4
Atoms
11,364
Mol. weight
163.45 kDa
Released
18 Dec 2024

Explore 9C5C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C5C contains 96 α-helices and 14 β-strands across 4 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: 47 helices, 0 β-strands

ElementResiduesLengthSheet
α-helix48-525
α-helix56-7217
α-helix77-793
α-helix80-856
α-helix92-10514
α-helix110-1156
α-helix117-1237
α-helix129-14113
α-helix148-16013
α-helix164-18017
α-helix182-1843
α-helix185-19612
α-helix201-21414
α-helix220-2245
α-helix226-2327
α-helix238-25518
α-helix295-30410
α-helix305-3095
α-helix313-32614
α-helix332-3343
α-helix335-3417
α-helix342-3443
α-helix347-36317
α-helix373-3753
α-helix377-3782
α-helix383-39513
α-helix402-41312
α-helix418-43417
α-helix436-4383
α-helix439-4479
α-helix448-4514
α-helix455-47117
α-helix477-48610
α-helix487-4893
α-helix493-50513
α-helix514-52411
α-helix525-5273
α-helix530-56334
α-helix568-58114
α-helix584-5863
α-helix589-5924
α-helix594-5985
α-helix601-6055
α-helix612-6165
α-helix622-6265
α-helix635-6406
α-helix646-6494
Chain D: 38 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix19-279
α-helix32-4615
α-helix52-6817
α-helix73-753
α-helix76-838
α-helix88-9912
α-helix107-1126
α-helix113-1219
α-helix125-13511
α-helix141-15414
α-helix160-17617
α-helix178-19114
α-helix197-21115
α-helix215-2217
α-helix222-23110
α-helix235-24814
α-helix253-26917
α-helix273-29018
α-helix298-31316
α-helix317-33317
α-helix335-3384
α-helix343-3486
α-helix354-36714
α-helix373-38614
α-helix390-40516
α-helix415-42612
α-helix434-44714
α-helix452-46413
α-helix466-4694
α-helix478-49114
α-helix493-4953
α-helix499-5068
α-helix509-5135
α-helix516-54025
α-helix543-55412
α-helix558-5614
α-helix566-58722
α-helix592-5998
Chain M: 6 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand2-871
β-strand14-1961
α-helix23-253
α-helix26-283
α-helix30-389
β-strand48-5031
β-strand55-6171
β-strand64-7071
α-helix76-9419
α-helix99-1046
α-helix106-11611
β-strand117-11822
β-strand121-12222
Chain S: 5 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand2-983
β-strand14-1963
α-helix25-4016
β-strand49-5133
β-strand61-6883
β-strand71-7883
α-helix83-10018
α-helix106-1116
α-helix113-12311
β-strand124-12524
β-strand128-12924
α-helix134-15017

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
AP-3 complex subunit delta-1Dprotein588Homo sapiensO14617 (AlphaFold model)
AP-3 complex subunit beta-1Bprotein578Homo sapiensO00203 (AlphaFold model)
AP-3 complex subunit mu-1Mprotein124Homo sapiensQ9Y2T2 (AlphaFold model)
AP-3 complex subunit sigma-1Sprotein151Homo sapiensQ92572 (AlphaFold model)
Sequence of entity 1 (D), FASTA
>9C5C_1 AP-3 complex subunit delta-1 (chains D)
LQDLVRGIRNHKEDEAKYISQCIDEIKQELKQDNIAVKANAVCKLTYLQMLGYDISWAAF
NIIEVMSASKFTFKRIGYLAASQSFHEGTDVIMLTTNQIRKDLSSPSQYDTGVALTGLSC
FVTPDLARDLANDIMTLMSHTKPYIRKKAVLIMYKVFLKYPESLRPAFPRLKEKLEDPDP
GVQSAAVNVICELARRNPKNYLSLAPLFFKLMTSSTNNWVLIKIIKLFGALTPLEPRLGK
KLIEPLTNLIHSTSAMSLLYECVNTVIAVLISLSSGMPNHSASIQLCVQKLRILIEDSDQ
NLKYLGLLAMSKILKTHPKSVQSHKDLILQCLDDKDESIRLRALDLLYGMVSKKNLMEIV
KKLMTHVDKAEGTTYRDELLTKIIDICSQSNYQYITNFEWYISILVELTRLEGTRHGHLI
AAQMLDVAIRVKAIRKFAVSQMSALLDSAHLLASSTQRNGICEVLYAAAWICGEFSEHLQ
EPHHTLEAMLRPRVTTLPGHIQAVYVQNVVKLYASILQQKEQAGEAEGAQAVTQLMVDRL
PQFVQSADLEVQERASCILQLVKHIQKLQAKDVPVAEEVSALFAGELN
Sequence of entity 2 (B), FASTA
>9C5C_2 AP-3 complex subunit beta-1 (chains B)
DLKKNEDLKQMLESNKDSAKLDAMKRIVGMIAKGKNASELFPAVVKNVASKNIEIKKLVY
VYLVRYAEEQQDLALLSISTFQRALKDPNQLIRASALRVLSSIRVPIIVPIMMLAIKEAS
ADLSPYVRKNAAHAIQKLYSLDPEQKEMLIEVIEKLLKDKSTLVAGSVVMAFEEVCPDRI
DLIHKNYRKLCNLLVDVEEWGQVVIIHMLTRYARTQFVSPWDPDHRLLIRNTKPLLQSRN
AAVVMAVAQLYWHISPKSEAGIISKSLVRLLRSNREVQYIVLQNIATMSIQRKGMFEPYL
KSFYVRSTDPTMIKTLKLEILTNLANEANISTLLREFQTYVKSQDKQFAAATIQTIGRCA
TNILEVTDTCLNGLVCLLSNRDEIVVAESVVVIKKLLQMQPAQHGEIIKHMAKLLDSITV
PVARASILWLIGENCERVPKIAPDVLRKMAKSFTSEDDLVKLQILNLGAKLYLTNSKQTK
LLTQYILNLGKYDQNYDIRDRTRFIRQLIVPNVKSGALSKYAKKIFLAQKPAPLLESPFK
DRDHFQLGTLSHTLNIKATGYLELSNWPEVAPDPSVRN
Sequence of entity 3 (M), FASTA
>9C5C_3 AP-3 complex subunit mu-1 (chains M)
MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIY
RDKLFFVSVIQTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNG
FPLA
Sequence of entity 4 (S), FASTA
>9C5C_4 AP-3 complex subunit sigma-1 (chains S)
MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSD
NKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHVDKVHNIL
AEMVMGGMVLETNMNEIVTQIDAQNKLEKSE

Primary citation

A structure-based mechanism for initiation of AP-3 coated vesicle formation. Begley, M., Aragon, M., Baker, R.W. Proc Natl Acad Sci U S A (2024) 121:e2411974121-e2411974121. DOI 10.1073/pnas.2411974121 · PubMed

Other PDB entries of the same protein (UniProt O14617 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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