9C58: AP-3

AP-3 bound to myristoylated Arf1 (Q71L). Determined by electron microscopy at 4.7 Å resolution. Released 18 Dec 2024.

Method: Electron microscopy
Resolution: 4.7 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,954
Mol. weight: 235.95 kDa
Ligands: GTP, MG
Released: 18 Dec 2024

Explore 9C58 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C58 contains 104 α-helices and 22 β-strands across 5 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 A: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-23	5	5
α-helix	30-39	10
β-strand	51-58	8	5
β-strand	61-68	8	5
α-helix	72-81	10
β-strand	87-93	7	5
α-helix	97-99	3
α-helix	100-111	12
α-helix	114-116	3
β-strand	120-126	7	5
α-helix	136-143	8
α-helix	145-147	3
β-strand	153-157	5	5
β-strand	159	1	6
β-strand	164	1	6
α-helix	166-177	12

Chain B: 46 helices, 0 β-strands

Element	Residues	Length
α-helix	49-52	4
α-helix	56-71	16
α-helix	77-79	3
α-helix	80-84	5
α-helix	92-105	14
α-helix	110-115	6
α-helix	117-123	7
α-helix	129-141	13
α-helix	148-160	13
α-helix	164-180	17
α-helix	182-184	3
α-helix	185-196	12
α-helix	201-214	14
α-helix	220-223	4
α-helix	226-232	7
α-helix	238-255	18
α-helix	295-304	10
α-helix	305-309	5
α-helix	313-325	13
α-helix	332-335	4
α-helix	336-342	7
α-helix	347-363	17
α-helix	369-371	3
α-helix	373-375	3
α-helix	377-378	2
α-helix	383-396	14
α-helix	402-413	12
α-helix	418-434	17
α-helix	436-438	3
α-helix	439-449	11
α-helix	455-471	17
α-helix	477-486	10
α-helix	487-489	3
α-helix	493-505	13
α-helix	514-524	11
α-helix	525-527	3
α-helix	530-563	34
α-helix	569-581	13
α-helix	584-586	3
α-helix	589-592	4
α-helix	594-599	6
α-helix	601-605	5
α-helix	612-616	5
α-helix	622-626	5
α-helix	638-640	3
α-helix	646-649	4

Chain D: 39 helices, 0 β-strands

Element	Residues	Length
α-helix	19-27	9
α-helix	32-47	16
α-helix	52-68	17
α-helix	73-75	3
α-helix	76-83	8
α-helix	88-101	14
α-helix	107-112	6
α-helix	113-121	9
α-helix	125-135	11
α-helix	141-154	14
α-helix	160-176	17
α-helix	181-191	11
α-helix	197-211	15
α-helix	215-221	7
α-helix	222-231	10
α-helix	235-248	14
α-helix	253-269	17
α-helix	273-290	18
α-helix	298-312	15
α-helix	317-333	17
α-helix	335-338	4
α-helix	343-346	4
α-helix	348-350	3
α-helix	354-366	13
α-helix	373-385	13
α-helix	390-405	16
α-helix	415-426	12
α-helix	434-447	14
α-helix	452-464	13
α-helix	466-469	4
α-helix	478-491	14
α-helix	493-495	3
α-helix	499-506	8
α-helix	509-513	5
α-helix	516-540	25
α-helix	543-553	11
α-helix	557-561	5
α-helix	566-587	22
α-helix	592-598	7

Chain M: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	14-19	6	1
α-helix	26-28	3
α-helix	29-38	10
β-strand	48-50	3	1
β-strand	55-61	7	1
β-strand	64-70	7	1
α-helix	76-94	19
α-helix	99-104	6
α-helix	106-116	11
β-strand	117-118	2	2
β-strand	121-122	2	2

Chain S: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	3
β-strand	14-19	6	3
α-helix	25-40	16
β-strand	49-51	3	3
α-helix	54-56	3
β-strand	62-68	7	3
β-strand	71-77	7	3
α-helix	83-100	18
α-helix	106-111	6
α-helix	113-123	11
β-strand	124-125	2	4
β-strand	128-129	2	4
α-helix	134-150	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-3 complex subunit delta-1	D	protein	617	Homo sapiens	O14617 (AlphaFold model)
AP-3 complex subunit beta-1	B	protein	677	Homo sapiens	O00203 (AlphaFold model)
AP-3 complex subunit mu-1	M	protein	418	Homo sapiens	Q9Y2T2 (AlphaFold model)
AP-3 complex subunit sigma-1	S	protein	193	Homo sapiens	Q92572 (AlphaFold model)
ADP-ribosylation factor 1	A	protein	182	Homo sapiens	P84077

Sequence of entity 1 (D), FASTA

>9C58_1 AP-3 complex subunit delta-1 (chains D)
MALKMVKGSIDRMFDKNLQDLVRGIRNHKEDEAKYISQCIDEIKQELKQDNIAVKANAVC
KLTYLQMLGYDISWAAFNIIEVMSASKFTFKRIGYLAASQSFHEGTDVIMLTTNQIRKDL
SSPSQYDTGVALTGLSCFVTPDLARDLANDIMTLMSHTKPYIRKKAVLIMYKVFLKYPES
LRPAFPRLKEKLEDPDPGVQSAAVNVICELARRNPKNYLSLAPLFFKLMTSSTNNWVLIK
IIKLFGALTPLEPRLGKKLIEPLTNLIHSTSAMSLLYECVNTVIAVLISLSSGMPNHSAS
IQLCVQKLRILIEDSDQNLKYLGLLAMSKILKTHPKSVQSHKDLILQCLDDKDESIRLRA
LDLLYGMVSKKNLMEIVKKLMTHVDKAEGTTYRDELLTKIIDICSQSNYQYITNFEWYIS
ILVELTRLEGTRHGHLIAAQMLDVAIRVKAIRKFAVSQMSALLDSAHLLASSTQRNGICE
VLYAAAWICGEFSEHLQEPHHTLEAMLRPRVTTLPGHIQAVYVQNVVKLYASILQQKEQA
GEAEGAQAVTQLMVDRLPQFVQSADLEVQERASCILQLVKHIQKLQAKDVPVAEEVSALF
AGELNPVAPKAQKKVPV

Sequence of entity 2 (B), FASTA

>9C58_2 AP-3 complex subunit beta-1 (chains B)
MSSNSFPYNEQSGGGEATELGQEATSTISPSGAFGLFSSDLKKNEDLKQMLESNKDSAKL
DAMKRIVGMIAKGKNASELFPAVVKNVASKNIEIKKLVYVYLVRYAEEQQDLALLSISTF
QRALKDPNQLIRASALRVLSSIRVPIIVPIMMLAIKEASADLSPYVRKNAAHAIQKLYSL
DPEQKEMLIEVIEKLLKDKSTLVAGSVVMAFEEVCPDRIDLIHKNYRKLCNLLVDVEEWG
QVVIIHMLTRYARTQFVSPWKEGDELEDNGKNFYESDDDQKEKTDKKKKPYTMDPDHRLL
IRNTKPLLQSRNAAVVMAVAQLYWHISPKSEAGIISKSLVRLLRSNREVQYIVLQNIATM
SIQRKGMFEPYLKSFYVRSTDPTMIKTLKLEILTNLANEANISTLLREFQTYVKSQDKQF
AAATIQTIGRCATNILEVTDTCLNGLVCLLSNRDEIVVAESVVVIKKLLQMQPAQHGEII
KHMAKLLDSITVPVARASILWLIGENCERVPKIAPDVLRKMAKSFTSEDDLVKLQILNLG
AKLYLTNSKQTKLLTQYILNLGKYDQNYDIRDRTRFIRQLIVPNVKSGALSKYAKKIFLA
QKPAPLLESPFKDRDHFQLGTLSHTLNIKATGYLELSNWPEVAPDPSVRNVEVIELAKEW
TPAGKAKQENSAKKFYS

Sequence of entity 3 (M), FASTA

>9C58_3 AP-3 complex subunit mu-1 (chains M)
MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIY
RDKLFFVSVIQTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNG
FPLATESNILKELIKPPTILRSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAY
FDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDLSLSFMNPRLLDDVSFHPCIRFK
RWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSISFKENSSCGRFDITIGPKQN
MGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLTWDVGKITPQKLPSLKGLVNL
QSGAPKPEENPSLNIQFKIQQLAISGLKVNRLDMYGEKYKPFKGVKYVTKAGKFQVRT

Sequence of entity 4 (S), FASTA

>9C58_4 AP-3 complex subunit sigma-1 (chains S)
MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSD
NKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHVDKVHNIL
AEMVMGGMVLETNMNEIVTQIDAQNKLEKSEAGLAGAPARAVSAVKNMNLPEIPRNINIG
DISIKVPNLPSFK

Sequence of entity 5 (A), FASTA

>9C58_5 ADP-ribosylation factor 1 (chains A)
GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNI
SFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVL
LVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK
SL

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1

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:

4AFI 2.8 Å, Complex between Vamp7 longin domain and fragment of delta-adaptin from AP3
9C5C 3.6 Å, Structure of Human Adaptor Protein Complex AP-3 in the Apo State
9C59 4.3 Å, Human AP-3 dimer bound to myristoylated Arf1 (Q71L) and LAMP1 cargo on a lipid nanodisc
9C5B 4.5 Å, AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map
9RTW 7.4 Å, Mammalian AP3 complex on tubular membranes (AP3 centered)

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