9C5A: AP-3 Arf1 dimeric interface, focused refinement

AP-3 Arf1 dimeric interface, focused refinement. Determined by electron microscopy at 4.2 Å resolution. Released 18 Dec 2024.

Method: Electron microscopy
Resolution: 4.2 Å
Organism: Homo sapiens
Chains: 8
Atoms: 15,806
Mol. weight: 293.95 kDa
Ligands: MG, GTP
Released: 18 Dec 2024

Explore 9C5A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C5A contains 116 α-helices and 80 β-strands across 8 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.

Chains b and B: 34 helices, 0 β-strands

Element	Residues	Length
α-helix	41-52	12
α-helix	56-71	16
α-helix	77-79	3
α-helix	80-83	4
α-helix	84-88	5
α-helix	92-105	14
α-helix	110-114	5
α-helix	118-123	6
α-helix	129-140	12
α-helix	145-147	3
α-helix	148-159	12
α-helix	164-180	17
α-helix	182-184	3
α-helix	185-196	12
α-helix	201-214	14
α-helix	219-221	3
α-helix	223-225	3
α-helix	226-232	7
α-helix	238-255	18
α-helix	296-304	9
α-helix	305-309	5
α-helix	313-326	14
α-helix	329-335	7
α-helix	336-342	7
α-helix	347-361	15
α-helix	365-367	3
α-helix	369-375	7
α-helix	383-396	14
α-helix	402-414	13
α-helix	418-426	9
α-helix	622-626	5
α-helix	633-640	8
α-helix	643-645	3
α-helix	646-648	3

Chains c and C: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
β-strand	16-24	9	20
α-helix	30-38	9
β-strand	43	1	10
β-strand	51-58	8	20
β-strand	61-68	8	20
α-helix	75-81	7
β-strand	87-93	7	20
α-helix	97-99	3
α-helix	100-111	12
α-helix	114-116	3
β-strand	120-126	7	20
α-helix	136-143	8
α-helix	145-147	3
β-strand	153-157	5	20
β-strand	159	1	21
β-strand	164	1	21
α-helix	166-177	12

Chains m and M: 14 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	12
β-strand	13-19	7	12
α-helix	26-28	3
α-helix	29-37	9
α-helix	42-44	3
β-strand	48-50	3	12
β-strand	55-61	7	12
β-strand	64-70	7	12
α-helix	76-94	19
α-helix	99-116	18
β-strand	117-118	2	13
β-strand	121-122	2	13
α-helix	127-133	7
β-strand	134	1	14
α-helix	135-137	3
α-helix	139-148	10
β-strand	153	1	14
α-helix	159-162	4
β-strand	178-191	14	15
β-strand	197-211	15	15
β-strand	217	1	16
β-strand	218-222	5	17
α-helix	225-227	3
β-strand	228-233	6	15
β-strand	237	1	17
α-helix	239-244	6
β-strand	248-250	3	17
β-strand	255-264	10	15
α-helix	269-271	3
β-strand	274-281	8	18
β-strand	288-297	10	18
β-strand	305-313	9	15
β-strand	318-325	8	18
β-strand	329-333	5	15
β-strand	338-346	9	15
β-strand	347	1	19
β-strand	350	1	19
β-strand	353-360	8	18
α-helix	364-367	4
α-helix	370-372	3
β-strand	373-380	8	15
β-strand	389-392	4	17
β-strand	395	1	16
β-strand	402-416	15	15

Chains y and Y: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	414	1
β-strand	415-416	2	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-3 complex subunit beta-1	B, b	protein	684	Homo sapiens	O00203 (AlphaFold model)
AP-3 complex subunit mu-1	M, m	protein	418	Homo sapiens	Q9Y2T2 (AlphaFold model)
ADP-ribosylation factor 1	C, c	protein	182	Homo sapiens	P84077 (AlphaFold model)
Lysosome-associated membrane glycoprotein 1	Y, y	protein	12	Homo sapiens	P11279 (AlphaFold model)

Sequence of entity 1 (B, b), FASTA

>9C5A_1 AP-3 complex subunit beta-1 (chains B, b)
MSSNSFPYNEQSGGGEATELGQEATSTISPSGAFGLFSSDLKKNEDLKQMLESNKDSAKL
DAMKRIVGMIAKGKNASELFPAVVKNVASKNIEIKKLVYVYLVRYAEEQQDLALLSISTF
QRALKDPNQLIRASALRVLSSIRVPIIVPIMMLAIKEASADLSPYVRKNAAHAIQKLYSL
DPEQKEMLIEVIEKLLKDKSTLVAGSVVMAFEEVCPDRIDLIHKNYRKLCNLLVDVEEWG
QVVIIHMLTRYARTQFVSPWKEGDELEDNGKNFYESDDDQKEKTDKKKKPYTMDPDHRLL
IRNTKPLLQSRNAAVVMAVAQLYWHISPKSEAGIISKSLVRLLRSNREVQYIVLQNIATM
SIQRKGMFEPYLKSFYVRSTDPTMIKTLKLEILTNLANEANISTLLREFQTYVKSQDKQF
AAATIQTIGRCATNILEVTDTCLNGLVCLLSNRDEIVVAESVVVIKKLLQMQPAQHGEII
KHMAKLLDSITVPVARASILWLIGENCERVPKIAPDVLRKMAKSFTSEDDLVKLQILNLG
AKLYLTNSKQTKLLTQYILNLGKYDQNYDIRDRTRFIRQLIVPNVKSGALSKYAKKIFLA
QKPAPLLESPFKDRDHFQLGTLSHTLNIKATGYLELSNWPEVAPDPSVRNVEVIELAKEW
TPAGKAKQENSAKKFYSGLEVLFQ

Sequence of entity 2 (M, m), FASTA

>9C5A_2 AP-3 complex subunit mu-1 (chains M, m)
MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIY
RDKLFFVSVIQTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNG
FPLATESNILKELIKPPTILRSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAY
FDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDLSLSFMNPRLLDDVSFHPCIRFK
RWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSISFKENSSCGRFDITIGPKQN
MGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLTWDVGKITPQKLPSLKGLVNL
QSGAPKPEENPSLNIQFKIQQLAISGLKVNRLDMYGEKYKPFKGVKYVTKAGKFQVRT

Sequence of entity 3 (C, c), FASTA

>9C5A_3 ADP-ribosylation factor 1 (chains C, c)
GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNI
SFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVL
LVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK
SL

Sequence of entity 4 (Y, y), FASTA

>9C5A_4 Lysosome-associated membrane glycoprotein 1 (chains Y, y)
GRKRSHAGYQTI

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

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 O00203 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
9C58 4.7 Å, AP-3 bound to myristoylated Arf1 (Q71L)

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