9C5B: AP-3
AP-3 bound to myristoylated Arf1 (Q71L) and LAMPI on a lipid nanodisc; combined map. Determined by electron microscopy at 4.5 Å resolution. Released 18 Dec 2024.
- Method
- Electron microscopy
- Resolution
- 4.5 Å
- Organism
- Homo sapiens
- Chains
- 7
- Atoms
- 16,874
- Mol. weight
- 258.65 kDa
- Ligands
- GTP, MG
- Released
- 18 Dec 2024
Explore 9C5B in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9C5B contains 133 α-helices and 50 β-strands across 7 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: 9 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-23 | 6 | 1 |
| α-helix | 30-39 | 10 | |
| β-strand | 51-58 | 8 | 1 |
| β-strand | 61-68 | 8 | 1 |
| α-helix | 72-81 | 10 | |
| β-strand | 87-93 | 7 | 1 |
| α-helix | 97-99 | 3 | |
| α-helix | 100-111 | 12 | |
| α-helix | 114-116 | 3 | |
| β-strand | 120-126 | 7 | 1 |
| α-helix | 133-135 | 3 | |
| α-helix | 136-143 | 8 | |
| α-helix | 145-147 | 3 | |
| β-strand | 153-157 | 5 | 1 |
| α-helix | 166-177 | 12 | |
Chain B: 50 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-52 | 13 | |
| 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 | 110-113 | 4 | |
| α-helix | 114-116 | 3 | |
| α-helix | 117-123 | 7 | |
| α-helix | 129-141 | 13 | |
| α-helix | 145-147 | 3 | |
| α-helix | 148-159 | 12 | |
| α-helix | 164-180 | 17 | |
| α-helix | 182-184 | 3 | |
| α-helix | 185-195 | 11 | |
| α-helix | 201-214 | 14 | |
| α-helix | 219-221 | 3 | |
| α-helix | 223-225 | 3 | |
| α-helix | 226-233 | 8 | |
| α-helix | 238-255 | 18 | |
| α-helix | 295-304 | 10 | |
| α-helix | 305-309 | 5 | |
| β-strand | 310 | 1 | 7 |
| α-helix | 313-325 | 13 | |
| α-helix | 332-334 | 3 | |
| α-helix | 335-342 | 8 | |
| α-helix | 347-361 | 15 | |
| α-helix | 365-367 | 3 | |
| α-helix | 369-375 | 7 | |
| α-helix | 376-378 | 3 | |
| α-helix | 383-396 | 14 | |
| α-helix | 402-413 | 12 | |
| α-helix | 418-434 | 17 | |
| α-helix | 436-438 | 3 | |
| α-helix | 439-448 | 10 | |
| α-helix | 449-451 | 3 | |
| α-helix | 455-471 | 17 | |
| α-helix | 477-486 | 10 | |
| α-helix | 493-505 | 13 | |
| α-helix | 514-524 | 11 | |
| α-helix | 525-527 | 3 | |
| α-helix | 530-564 | 35 | |
| α-helix | 568-581 | 14 | |
| α-helix | 591-593 | 3 | |
| α-helix | 594-598 | 5 | |
| α-helix | 600-605 | 6 | |
| α-helix | 610-614 | 5 | |
| α-helix | 618 | 1 | |
| α-helix | 622-626 | 5 | |
| α-helix | 633-640 | 8 | |
| α-helix | 646-649 | 4 | |
Chain C: 9 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-13 | 9 | |
| β-strand | 19-24 | 6 | 2 |
| α-helix | 30-38 | 9 | |
| α-helix | 42-44 | 3 | |
| β-strand | 51-58 | 8 | 2 |
| β-strand | 61-68 | 8 | 2 |
| α-helix | 75-81 | 7 | |
| β-strand | 87-93 | 7 | 2 |
| α-helix | 100-111 | 12 | |
| α-helix | 119 | 1 | |
| β-strand | 120-126 | 7 | 2 |
| α-helix | 136-143 | 8 | |
| α-helix | 145-147 | 3 | |
| β-strand | 153-157 | 5 | 2 |
| β-strand | 159 | 1 | 3 |
| β-strand | 164 | 1 | 3 |
| α-helix | 166-176 | 11 | |
Chain D: 41 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-13 | 12 | |
| α-helix | 18-27 | 10 | |
| α-helix | 32-46 | 15 | |
| α-helix | 52-67 | 16 | |
| α-helix | 73-75 | 3 | |
| α-helix | 76-83 | 8 | |
| α-helix | 88-101 | 14 | |
| α-helix | 108-111 | 4 | |
| α-helix | 113-121 | 9 | |
| α-helix | 125-137 | 13 | |
| α-helix | 141-154 | 14 | |
| α-helix | 160-176 | 17 | |
| α-helix | 178-191 | 14 | |
| α-helix | 197-213 | 17 | |
| α-helix | 215-217 | 3 | |
| α-helix | 222-231 | 10 | |
| α-helix | 235-248 | 14 | |
| α-helix | 253-269 | 17 | |
| α-helix | 273-291 | 19 | |
| α-helix | 297-313 | 17 | |
| α-helix | 317-331 | 15 | |
| α-helix | 335-338 | 4 | |
| α-helix | 339-341 | 3 | |
| α-helix | 342-348 | 7 | |
| α-helix | 354-367 | 14 | |
| α-helix | 373-386 | 14 | |
| α-helix | 390-409 | 20 | |
| α-helix | 415-425 | 11 | |
| α-helix | 434-447 | 14 | |
| α-helix | 449-451 | 3 | |
| α-helix | 452-464 | 13 | |
| α-helix | 466-469 | 4 | |
| α-helix | 480-491 | 12 | |
| α-helix | 493-495 | 3 | |
| α-helix | 499-506 | 8 | |
| α-helix | 509-513 | 5 | |
| α-helix | 516-540 | 25 | |
| α-helix | 543-554 | 12 | |
| α-helix | 557-560 | 4 | |
| α-helix | 566-587 | 22 | |
| α-helix | 593-601 | 9 | |
Chain M: 17 helices, 27 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-9 | 6 | 4 |
| β-strand | 14-19 | 6 | 4 |
| α-helix | 23-25 | 3 | |
| α-helix | 26-28 | 3 | |
| α-helix | 29-38 | 10 | |
| α-helix | 42-44 | 3 | |
| β-strand | 48-50 | 3 | 4 |
| β-strand | 55-61 | 7 | 4 |
| β-strand | 64-70 | 7 | 4 |
| α-helix | 76-94 | 19 | |
| α-helix | 99-104 | 6 | |
| α-helix | 106-116 | 11 | |
| β-strand | 117-118 | 2 | 5 |
| β-strand | 121-122 | 2 | 5 |
| α-helix | 127-133 | 7 | |
| β-strand | 134 | 1 | 6 |
| α-helix | 139-148 | 10 | |
| β-strand | 153 | 1 | 6 |
| α-helix | 159-162 | 4 | |
| β-strand | 178-191 | 14 | 7 |
| β-strand | 197-211 | 15 | 7 |
| β-strand | 217-222 | 6 | 8 |
| α-helix | 225-227 | 3 | |
| β-strand | 229-233 | 5 | 7 |
| α-helix | 239-244 | 6 | |
| β-strand | 248-250 | 3 | 8 |
| α-helix | 252-253 | 2 | |
| β-strand | 255-264 | 10 | 7 |
| α-helix | 269-271 | 3 | |
| β-strand | 274-281 | 8 | 9 |
| β-strand | 288-297 | 10 | 9 |
| α-helix | 303-305 | 3 | |
| β-strand | 306-313 | 8 | 7 |
| β-strand | 318-325 | 8 | 9 |
| β-strand | 329-333 | 5 | 7 |
| β-strand | 338-344 | 7 | 7 |
| β-strand | 347 | 1 | 10 |
| β-strand | 350 | 1 | 10 |
| β-strand | 353-360 | 8 | 9 |
| α-helix | 364-367 | 4 | |
| α-helix | 370-372 | 3 | |
| β-strand | 373-380 | 8 | 7 |
| β-strand | 389-395 | 7 | 8 |
| β-strand | 402-416 | 15 | 7 |
Chain S: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-9 | 8 | 11 |
| β-strand | 14-19 | 6 | 11 |
| α-helix | 25-40 | 16 | |
| β-strand | 49-51 | 3 | 11 |
| α-helix | 52 | 1 | |
| β-strand | 62-68 | 7 | 11 |
| β-strand | 71-77 | 7 | 11 |
| α-helix | 83-101 | 19 | |
| α-helix | 106-111 | 6 | |
| α-helix | 113-123 | 11 | |
| β-strand | 124-125 | 2 | 12 |
| β-strand | 128-129 | 2 | 12 |
| α-helix | 134-150 | 17 | |
Chain Y: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9 | 1 | |
| β-strand | 10-11 | 2 | 7 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| ADP-ribosylation factor 1 | A, C | protein | 182 | Homo sapiens | P84077 (AlphaFold model) |
| AP-3 complex subunit delta-1 | D | protein | 617 | Homo sapiens | O14617 (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) |
| Lysosome-associated membrane glycoprotein 1 | Y | protein | 12 | Homo sapiens | P11279 |
| AP-3 complex subunit beta-1 | B | protein | 677 | Homo sapiens | O00203 |
Sequence of entity 1 (A, C), FASTA
>9C5B_1 ADP-ribosylation factor 1 (chains A, C)
GNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNI
SFTVWDVGGLDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVL
LVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK
SL
Sequence of entity 2 (D), FASTA
>9C5B_2 AP-3 complex subunit delta-1 (chains D)
MALKMVKGSIDRMFDKNLQDLVRGIRNHKEDEAKYISQCIDEIKQELKQDNIAVKANAVC
KLTYLQMLGYDISWAAFNIIEVMSASKFTFKRIGYLAASQSFHEGTDVIMLTTNQIRKDL
SSPSQYDTGVALTGLSCFVTPDLARDLANDIMTLMSHTKPYIRKKAVLIMYKVFLKYPES
LRPAFPRLKEKLEDPDPGVQSAAVNVICELARRNPKNYLSLAPLFFKLMTSSTNNWVLIK
IIKLFGALTPLEPRLGKKLIEPLTNLIHSTSAMSLLYECVNTVIAVLISLSSGMPNHSAS
IQLCVQKLRILIEDSDQNLKYLGLLAMSKILKTHPKSVQSHKDLILQCLDDKDESIRLRA
LDLLYGMVSKKNLMEIVKKLMTHVDKAEGTTYRDELLTKIIDICSQSNYQYITNFEWYIS
ILVELTRLEGTRHGHLIAAQMLDVAIRVKAIRKFAVSQMSALLDSAHLLASSTQRNGICE
VLYAAAWICGEFSEHLQEPHHTLEAMLRPRVTTLPGHIQAVYVQNVVKLYASILQQKEQA
GEAEGAQAVTQLMVDRLPQFVQSADLEVQERASCILQLVKHIQKLQAKDVPVAEEVSALF
AGELNPVAPKAQKKVPV
Sequence of entity 3 (M), FASTA
>9C5B_3 AP-3 complex subunit mu-1 (chains M)
MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIY
RDKLFFVSVIQTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNG
FPLATESNILKELIKPPTILRSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAY
FDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDLSLSFMNPRLLDDVSFHPCIRFK
RWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSISFKENSSCGRFDITIGPKQN
MGKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLTWDVGKITPQKLPSLKGLVNL
QSGAPKPEENPSLNIQFKIQQLAISGLKVNRLDMYGEKYKPFKGVKYVTKAGKFQVRT
Sequence of entity 4 (S), FASTA
>9C5B_4 AP-3 complex subunit sigma-1 (chains S)
MIKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSD
NKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHVDKVHNIL
AEMVMGGMVLETNMNEIVTQIDAQNKLEKSEAGLAGAPARAVSAVKNMNLPEIPRNINIG
DISIKVPNLPSFK
Sequence of entity 5 (Y), FASTA
>9C5B_5 Lysosome-associated membrane glycoprotein 1 (chains Y)
GRKRSHAGYQTI
Sequence of entity 6 (B), FASTA
>9C5B_6 AP-3 complex subunit beta-1 (chains B)
MSSNSFPYNEQSGGGEATELGQEATSTISPSGAFGLFSSDLKKNEDLKQMLESNKDSAKL
DAMKRIVGMIAKGKNASELFPAVVKNVASKNIEIKKLVYVYLVRYAEEQQDLALLSISTF
QRALKDPNQLIRASALRVLSSIRVPIIVPIMMLAIKEASADLSPYVRKNAAHAIQKLYSL
DPEQKEMLIEVIEKLLKDKSTLVAGSVVMAFEEVCPDRIDLIHKNYRKLCNLLVDVEEWG
QVVIIHMLTRYARTQFVSPWKEGDELEDNGKNFYESDDDQKEKTDKKKKPYTMDPDHRLL
IRNTKPLLQSRNAAVVMAVAQLYWHISPKSEAGIISKSLVRLLRSNREVQYIVLQNIATM
SIQRKGMFEPYLKSFYVRSTDPTMIKTLKLEILTNLANEANISTLLREFQTYVKSQDKQF
AAATIQTIGRCATNILEVTDTCLNGLVCLLSNRDEIVVAESVVVIKKLLQMQPAQHGEII
KHMAKLLDSITVPVARASILWLIGENCERVPKIAPDVLRKMAKSFTSEDDLVKLQILNLG
AKLYLTNSKQTKLLTQYILNLGKYDQNYDIRDRTRFIRQLIVPNVKSGALSKYAKKIFLA
QKPAPLLESPFKDRDHFQLGTLSHTLNIKATGYLELSNWPEVAPDPSVRNVEVIELAKEW
TPAGKAKQENSAKKFYS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 2 |
| MG | Magnesium ion | Mg | 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 P84077 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8SDW 1.75 Å, Crystal structure of the non-myristoylated mutant [L8K]Arf1 in complex with a GDP analogue
- 1HUR 2.0 Å, Human ADP-ribosylation factor 1 complexed with GDP, full length non-myristoylated
- 7R4H 2.34 Å, phospho-STING binding to adaptor protein complex-1
- 6FAE 2.35 Å, The Sec7 domain of IQSEC2 (Brag1) in complex with the small GTPase Arf1
- 1RE0 2.4 Å, Structure of ARF1-GDP bound to Sec7 domain complexed with Brefeldin A
- 9QLO 2.47 Å, NMT1-NAC bound human RNC with full length ARF1 - State 1
- 9QLQ 2.57 Å, NMT1-NAC bound human RNC with full length ARF1 - alternative State
- 7DN8 2.61 Å, Crystal structure of Salmonella effector SopF in complex with ARF1
- 9QLP 2.75 Å, NMT1-NAC bound human RNC with full length ARF1 - State 2
- 3O47 2.8 Å, Crystal structure of ARFGAP1-ARF1 fusion protein
- 7DN9 3.29 Å, Crystal structure of Salmonella effector in complex with NAD and host co-factor ARF1
- 6CM9 3.73 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit
Browse structure collections
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