6YAF: AP-2 complex subunit alpha-2

AP2 on a membrane containing tyrosine-based cargo peptide. Determined by electron microscopy at 9.1 Å resolution. Released 29 Jul 2020.

Method: Electron microscopy
Resolution: 9.1 Å
Organisms: Rattus norvegicus, Homo sapiens, Mus musculus
Chains: 5
Atoms: 14,145
Mol. weight: 245.95 kDa
Released: 29 Jul 2020

Explore 6YAF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YAF contains 91 α-helices and 38 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 A: 41 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-22	12
α-helix	26-37	12
α-helix	38-42	5
α-helix	43-44	2
α-helix	53-69	17
α-helix	77-83	7
α-helix	88-100	13
α-helix	106-121	16
α-helix	125-138	14
α-helix	141-146	6
α-helix	150-155	6
α-helix	163-178	16
α-helix	180-182	3
α-helix	189-195	7
α-helix	201-217	17
α-helix	224-238	15
β-strand	249	1	1
β-strand	252	1	1
α-helix	255-267	13
α-helix	276-291	16
α-helix	294-295	2
α-helix	300-317	18
α-helix	324-337	14
α-helix	343-356	14
α-helix	363-367	5
α-helix	370-378	9
α-helix	384-396	13
α-helix	399-413	15
α-helix	419-435	17
α-helix	439-452	14
α-helix	459-472	14
α-helix	476-488	13
α-helix	494-507	14
α-helix	508-510	3
α-helix	519-530	12
α-helix	535-551	17
α-helix	553-555	3
α-helix	556-563	8
α-helix	566-570	5
α-helix	575-587	13
α-helix	594-598	5
α-helix	605-607	3
α-helix	612-619	8

Chain B: 36 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	14-22	9
α-helix	27-42	16
α-helix	48-50	3
α-helix	51-57	7
α-helix	63-77	15
α-helix	84-95	12
α-helix	100-111	12
α-helix	117-130	14
α-helix	135-148	14
α-helix	156-167	12
α-helix	174-187	14
α-helix	201-213	13
α-helix	216-226	11
α-helix	234-244	11
α-helix	252-266	15
α-helix	275-283	9
α-helix	285-291	7
α-helix	296-312	17
α-helix	316-319	4
α-helix	321-324	4
α-helix	332-344	13
α-helix	351-362	12
α-helix	367-382	16
α-helix	385-399	15
α-helix	404-420	17
α-helix	427-434	8
α-helix	442-455	14
α-helix	462-469	8
α-helix	478-494	17
α-helix	496-498	3
α-helix	500-512	13
α-helix	517-530	14
α-helix	534-541	8
α-helix	557-563	7
α-helix	564-566	3
β-strand	567	1	2
β-strand	569	1	2
α-helix	570-574	5

Chain M: 10 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	3
β-strand	14	1	3
β-strand	18	1	3
α-helix	26-32	7
α-helix	33-37	5
β-strand	47-49	3	3
β-strand	54-58	5	3
β-strand	64-69	6	3
α-helix	75-93	19
α-helix	98-102	5
α-helix	105-115	11
β-strand	116-117	2	4
β-strand	120-121	2	4
α-helix	129-132	4
α-helix	145-156	12
β-strand	172-186	15	5
β-strand	190-205	16	5
β-strand	212	1	6
β-strand	213-216	4	7
β-strand	256-258	3	5
α-helix	265-271	7
β-strand	276	1	6
β-strand	281-290	10	5
β-strand	298-307	10	8
β-strand	311-320	10	8
β-strand	327-336	10	9
α-helix	337-338	2
β-strand	344-345	2	8
β-strand	352-356	5	9
β-strand	361-370	10	9
β-strand	374-382	9	8
α-helix	395-397	3
β-strand	398-402	5	9
β-strand	412-416	5	7
β-strand	430	1	5
β-strand	435-442	8	5
β-strand	443	1	9

Chain S: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	10
β-strand	16-19	4	10
α-helix	25-41	17
β-strand	49-51	3	10
β-strand	56-61	6	10
β-strand	65-70	6	10
α-helix	77-94	18
α-helix	100-117	18
β-strand	118-119	2	11
β-strand	122-123	2	11
α-helix	128-138	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-2 complex subunit alpha-2	A	protein	628	Rattus norvegicus	P18484 (AlphaFold model)
AP-2 complex subunit beta	B	protein	944	Homo sapiens	P63010 (AlphaFold model)
AP-2 complex subunit mu	M	protein	446	Rattus norvegicus	P84092 (AlphaFold model)
Tyrosine type cargo signal derived from TGN38	P	protein	16	Homo sapiens	O43493 (AlphaFold model)
AP-2 complex subunit sigma	S	protein	142	Mus musculus	P62743

Sequence of entity 1 (A), FASTA

>6YAF_1 AP-2 complex subunit alpha-2 (chains A)
MPAVSKGDGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA
STDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKV
QHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSE
FSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSI
REEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAA
KTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRAL
LLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLE
EMPPFPERESSILAKLKKKKGGSGLVPR

Sequence of entity 2 (B), FASTA

>6YAF_2 AP-2 complex subunit beta (chains B)
MHHHHHHMTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPD
VVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCI
RVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSN
PMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKD
DREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLS
GEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQ
VLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVV
IRDIFRKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGF
HDESTQVQLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTD
PVTAKEVVLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRKHL
PIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLLGDLLNLDLGPPVNVPQVSSMQMGAV
DLLGGGLDSLVGQSFIPSSVPATFAPSPTPAVVSSGLNDLFELSTGIGMAPGGYVAPKAV
WLPAVKAKGLEISGTFTHRQGHIYMEMNFTNKALQHMTDFAIQFNKNSFGVIPSTPLAIH
TPLMPNQSIDVSLPLNTLGPVMKMEPLNNLQVAVKNNIDVFYFSCLIPLNVLFVEDGKME
RQVFLATWKDIPNENELQFQIKECHLNADTVSSKLQNNNVYTIAKRNVEGQDMLYQSLKL
TNGIWILAELRIQPGNPNYTLSLKCRAPEVSQYIYQVYDSILKN

Sequence of entity 3 (M), FASTA

>6YAF_3 AP-2 complex subunit mu (chains M)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLES
VNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSMEQK
LISEEDLGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRV
IPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASEN
AIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEP
KLNYSDHDVIKWVRYIGRSGIYETRC

Sequence of entity 4 (P), FASTA

>6YAF_4 Tyrosine type cargo signal derived from TGN38 (chains P)
CKVTRRPKASDYQRLN

Sequence of entity 5 (S), FASTA

>6YAF_5 AP-2 complex subunit sigma (chains S)
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYR
RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLMLQSLE

Primary citation

Architecture of the AP2/clathrin coat on the membranes of clathrin-coated vesicles. Kovtun, O., Dickson, V.K., Kelly, B.T. et al. Sci Adv (2020) 6:eaba8381-eaba8381. DOI 10.1126/sciadv.aba8381 · PubMed

Other PDB entries of the same protein (UniProt P18484 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6QH5 2.56 Å, AP2 clathrin adaptor mu2T156-phosphorylated core in closed conformation
2VGL 2.6 Å, AP2 clathrin adaptor core
4UQI 2.79 Å, AP2 controls clathrin polymerization with a membrane-activated switch
7OHO 2.88 Å, Crystal structure of AP2 FCHO2 chimera
4NEE 2.88 Å, crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef
6URI 3.0 Å, HIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 clathrin adaptor complex
2XA7 3.1 Å, AP2 clathrin adaptor core in active complex with cargo peptides
7OG1 3.25 Å, AP2 clathrin adaptor core in complex with cargo peptide and FCHO2
6QH7 3.4 Å, AP2 clathrin adaptor mu2T156-phosphorylated core with two cargo peptides in open+…
6OWT 3.8 Å, Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex
6YAE 3.9 Å, AP2 core in physiological buffer
7Z5C 4.16 Å, Chimera of AP2 with FCHO2 linker domain as a fusion on Cmu2 subunit

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