8T1O: AP2

AP2 bound to MSP2N2 nanodisc with Tgn38 cargo peptide; composite map. Determined by electron microscopy at 3.3 Å resolution. Released 12 Jul 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Mus musculus, Rattus norvegicus
Chains: 5
Atoms: 13,800
Mol. weight: 206.76 kDa
Ligands: PIO
Released: 12 Jul 2023

Explore 8T1O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T1O contains 93 α-helices and 36 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: 40 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-22	12
α-helix	26-44	19
α-helix	49-51	3
α-helix	52-68	17
α-helix	76-83	8
α-helix	88-100	13
α-helix	106-121	16
α-helix	125-137	13
α-helix	141-147	7
α-helix	151-153	3
α-helix	162-178	17
α-helix	180-182	3
α-helix	188-193	6
α-helix	194-197	4
α-helix	201-215	15
α-helix	224-237	14
β-strand	248-249	2	1
β-strand	252-253	2	1
α-helix	255-266	12
α-helix	269-271	3
α-helix	274-289	16
α-helix	294-295	2
α-helix	300-320	21
α-helix	324-338	15
α-helix	343-358	16
α-helix	363-367	5
α-helix	370-379	10
α-helix	383-396	14
α-helix	402-413	12
α-helix	421-434	14
α-helix	439-452	14
α-helix	458-472	15
α-helix	476-487	12
α-helix	494-507	14
α-helix	519-530	12
α-helix	535-551	17
α-helix	553-555	3
α-helix	556-564	9
α-helix	566-569	4
α-helix	574-589	16
α-helix	594-598	5
α-helix	603-605	3

Chain B: 37 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	14-22	9
α-helix	27-43	17
α-helix	48-50	3
α-helix	51-57	7
α-helix	63-77	15
α-helix	87-95	9
α-helix	100-111	12
α-helix	116-130	15
α-helix	135-150	16
α-helix	156-167	12
α-helix	174-187	14
α-helix	201-213	13
α-helix	216-228	13
α-helix	234-244	11
α-helix	245-248	4
α-helix	253-265	13
α-helix	275-291	17
α-helix	296-312	17
α-helix	322-324	3
α-helix	332-345	14
α-helix	351-361	11
α-helix	367-383	17
α-helix	388-400	13
α-helix	404-420	17
α-helix	426-428	3
α-helix	429-434	6
α-helix	442-454	13
α-helix	462-468	7
α-helix	469-472	4
α-helix	478-494	17
α-helix	497-499	3
α-helix	500-511	12
α-helix	517-532	16
α-helix	534-541	8
α-helix	554-556	3
α-helix	557-565	9
β-strand	569	1	2
α-helix	570-574	5

Chain M: 11 helices, 25 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
β-strand	47-49	3	3
β-strand	54-60	7	3
β-strand	63-69	7	3
β-strand	74	1	2
α-helix	75-93	19
α-helix	98-103	6
α-helix	105-115	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	172-185	14	5
β-strand	191-205	15	5
β-strand	211-215	5	6
β-strand	245-248	4	5
α-helix	254-260	7
β-strand	263-265	3	6
α-helix	267-268	2
β-strand	270-279	10	5
α-helix	283-285	3
β-strand	287-296	10	7
β-strand	300-309	10	7
β-strand	318-325	8	5
β-strand	330-337	8	7
β-strand	341-345	5	5
β-strand	350-355	6	5
β-strand	363-364	2	7
β-strand	366-372	7	7
α-helix	383-385	3
β-strand	386-392	7	5
β-strand	403-407	5	6
β-strand	419-433	15	5

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3-4	2	5

Chain S: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	8
β-strand	14-19	6	8
α-helix	25-41	17
β-strand	49-52	4	8
β-strand	55-62	8	8
β-strand	65-71	7	8
α-helix	77-95	19
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	9
β-strand	122-123	2	9
α-helix	128-140	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-2 complex subunit alpha-2	A	protein	630	Mus musculus	P17427 (AlphaFold model)
AP-2 complex subunit beta	B	protein	591	Mus musculus	Q9DBG3 (AlphaFold model)
AP-2 complex subunit mu	M	protein	435	Mus musculus	P84091 (AlphaFold model)
AP-2 complex subunit sigma	S	protein	142	Mus musculus	P62743 (AlphaFold model)
Trans-Golgi network integral membrane protein TGN38	P	protein	14	Rattus norvegicus	P19814

Sequence of entity 1 (A), FASTA

>8T1O_1 AP-2 complex subunit alpha-2 (chains A)
MPAVSKGDGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA
STDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKV
QHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSE
FSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSI
REEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAA
KTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRAL
LLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLE
EMPPFPERESSILAKLKKKKGGSGLEVLFQ

Sequence of entity 2 (B), FASTA

>8T1O_2 AP-2 complex subunit beta (chains B)
MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANA
VAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQY
VALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRK
YPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQV
QLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEV
VLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRK

Sequence of entity 3 (M), FASTA

>8T1O_3 AP-2 complex subunit mu (chains M)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLES
VNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQS
IAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTK
LEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAG
MKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIK
WVRYIGRSGIYETRC

Sequence of entity 4 (S), FASTA

>8T1O_4 AP-2 complex subunit sigma (chains S)
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYR
RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLMLQSLE

Sequence of entity 5 (P), FASTA

>8T1O_5 Trans-Golgi network integral membrane protein TGN38 (chains P)
KVTRRPKASDYQRL

Ligands and cofactors

ID	Name	Formula	Copies
PIO	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-d…	C25 H49 O19 P3	1

Primary citation

Lipid nanodiscs as a template for high-resolution cryo-EM structures of peripheral membrane proteins. S Cannon, K., Sarsam, R.D., Tedamrongwanish, T. et al. J Struct Biol (2023) 215:107989-107989. DOI 10.1016/j.jsb.2023.107989 · PubMed

Other PDB entries of the same protein (UniProt P17427 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1KYF 1.22 Å, Ap-2 clathrin adaptor alpha-appendage in complex with EPS15 dpf peptide
1QTS 1.4 Å, Crystal structure of the ap-2 clathrin adaptor alpha-appendage
7OHI 1.41 Å, FCHO1-peptide-AP2 alpha ear complex
1QTP 1.6 Å, Crystal structure of the ap-2 clathrin adaptor alpha-appendage
2VJ0 1.6 Å, Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex,…
1KYU 1.8 Å, Ap-2 clathrin adaptor alpha-appendage in complex with EPS15 dpf peptide
1B9K 1.9 Å, Alpha-adaptin appendage domain, from clathrin adaptor AP2
1W80 1.9 Å, Crystal structure of the alpha-adaptin appendage domain, from the AP2 adaptor complex,…
3HS8 1.9 Å, Intersectin 1-peptide-AP2 alpha ear complex
9PUE 1.91 Å, Structure of Alpha Appendage of AP2 bound to the FxDxF motif derived of CCDC32
1KY6 2.0 Å, Ap-2 clathrin adaptor alpha-appendage in complex with epsin dpw peptide
1KYD 2.0 Å, Ap-2 clathrin adaptor alpha-appendage in complex with epsin dpw peptide

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