6YAE: AP2 core in physiological buffer

AP2 core in physiological buffer. Determined by electron microscopy at 3.9 Å resolution. Released 29 Jul 2020.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Rattus norvegicus, Homo sapiens, Mus musculus
Chains: 4
Atoms: 13,707
Mol. weight: 203.37 kDa
Released: 29 Jul 2020

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

Secondary structure: helices and β-sheets

6YAE contains 95 α-helices and 36 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	11-21	11
α-helix	26-45	20
α-helix	52-68	17
α-helix	76-81	6
α-helix	88-100	13
α-helix	106-121	16
α-helix	125-138	14
α-helix	141-147	7
α-helix	151-156	6
α-helix	162-178	17
α-helix	189-194	6
α-helix	195-197	3
α-helix	201-215	15
α-helix	219-221	3
α-helix	225-237	13
α-helix	245-247	3
β-strand	248-249	2	1
β-strand	252-253	2	1
α-helix	255-266	12
α-helix	274-290	17
α-helix	294-295	2
α-helix	300-320	21
α-helix	324-337	14
α-helix	343-356	14
α-helix	363-368	6
α-helix	370-379	10
α-helix	383-395	13
α-helix	402-413	12
α-helix	418-435	18
α-helix	439-453	15
α-helix	454-456	3
α-helix	459-471	13
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	566-569	4
α-helix	574-587	14
α-helix	595-598	4
α-helix	604-607	4

Chain B: 39 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	14-21	8
α-helix	27-43	17
α-helix	48-50	3
α-helix	51-56	6
α-helix	63-77	15
α-helix	81-85	5
α-helix	88-92	5
α-helix	100-112	13
α-helix	118-130	13
α-helix	135-150	16
α-helix	157-169	13
α-helix	174-189	16
α-helix	200-213	14
α-helix	218-228	11
α-helix	234-244	11
α-helix	252-265	14
α-helix	277-283	7
α-helix	285-290	6
α-helix	296-312	17
α-helix	325-327	3
α-helix	332-345	14
α-helix	351-361	11
α-helix	367-380	14
α-helix	385-387	3
α-helix	388-400	13
α-helix	404-420	17
α-helix	429-434	6
α-helix	442-453	12
α-helix	456-458	3
α-helix	462-471	10
α-helix	478-494	17
α-helix	500-508	9
α-helix	509-513	5
α-helix	517-532	16
α-helix	536-541	6
α-helix	545-547	3
α-helix	557-565	9
β-strand	569	1	2
α-helix	570-574	5
α-helix	578-580	3

Chain M: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	3
β-strand	14-19	6	3
α-helix	26-32	7
α-helix	33-37	5
α-helix	43-44	2
β-strand	47-50	4	3
β-strand	53-60	8	3
β-strand	63-69	7	3
β-strand	74	1	2
α-helix	75-93	19
α-helix	98-103	6
α-helix	105-114	10
β-strand	116-117	2	4
β-strand	120-121	2	4
α-helix	126-128	3
β-strand	172-185	14	5
β-strand	191-205	15	5
β-strand	211-216	6	6
β-strand	245-248	4	5
β-strand	253	1	6
β-strand	263-265	3	6
α-helix	267-268	2
β-strand	270-279	10	5
β-strand	287-294	8	7
β-strand	300-309	10	7
β-strand	317-325	9	5
β-strand	330-337	8	7
β-strand	341-345	5	5
β-strand	350-358	9	5
β-strand	363-372	10	7
α-helix	383-385	3
β-strand	386-392	7	5
β-strand	401-407	7	6
β-strand	414	1	6
α-helix	415-417	3
β-strand	419-433	15	5

Chain S: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	8
β-strand	14-19	6	8
α-helix	25-39	15
β-strand	49-52	4	8
β-strand	55-61	7	8
β-strand	65-71	7	8
α-helix	78-94	17
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	9
β-strand	122-123	2	9
α-helix	128-138	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-2 complex subunit alpha	A	protein	621	Rattus norvegicus	P18484 (AlphaFold model)
AP-2 complex subunit beta	B	protein	591	Homo sapiens	P63010 (AlphaFold model)
AP-2 complex subunit mu	M	protein	435	Rattus norvegicus	P84092 (AlphaFold model)
AP-2 complex subunit sigma	S	protein	142	Mus musculus	P62743 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6YAE_1 AP-2 complex subunit alpha (chains A)
MPAVSKGEGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA
STDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKV
QHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSE
FSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSI
REEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAA
KTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRAL
LLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLE
EMPPFPERESSILAKLKKKKG

Sequence of entity 2 (B), FASTA

>6YAE_2 AP-2 complex subunit beta (chains B)
MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANA
VAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQY
VALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRK
YPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQV
QLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEV
VLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRK

Sequence of entity 3 (M), FASTA

>6YAE_3 AP-2 complex subunit mu (chains M)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLES
VNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQS
IAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTK
LEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAG
MKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIK
WVRYIGRSGIYETRC

Sequence of entity 4 (S), FASTA

>6YAE_4 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
7Z5C 4.16 Å, Chimera of AP2 with FCHO2 linker domain as a fusion on Cmu2 subunit
6QH6 5.0 Å, AP2 clathrin adaptor core with two cargo peptides in open+ conformation

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