7OG1: AP2 clathrin adaptor core

Name: PDB 7OG1: AP2 clathrin adaptor core in complex with cargo peptide and FCHO2
Published: 2022-06-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: endocytosis

AP2 clathrin adaptor core in complex with cargo peptide and FCHO2. Determined by X-ray diffraction at 3.25 Å resolution. Released 1 Jun 2022.

Method: X-ray diffraction
Resolution: 3.25 Å
Organisms: Rattus norvegicus, Homo sapiens, Mus musculus
Chains: 8
Atoms: 14,391
Mol. weight: 290.77 kDa
Released: 1 Jun 2022

Explore 7OG1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OG1 contains 101 α-helices and 46 β-strands across 6 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 AAA: 44 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-22	12
α-helix	29-36	8
α-helix	41-44	4
α-helix	54-57	4
α-helix	77-80	4
α-helix	82-84	3
α-helix	109-112	4
α-helix	117-120	4
α-helix	133-138	6
α-helix	142-145	4
α-helix	150-155	6
α-helix	162-169	8
α-helix	172-178	7
α-helix	189-192	4
α-helix	194-196	3
α-helix	201-214	14
α-helix	219-222	4
α-helix	223-229	7
α-helix	231-234	4
β-strand	248-249	2	1
β-strand	252-253	2	1
α-helix	259-262	4
α-helix	276-287	12
α-helix	301-320	20
α-helix	324-328	5
α-helix	331-334	4
α-helix	343-351	9
α-helix	353-356	4
α-helix	360-366	7
α-helix	367-369	3
α-helix	370-377	8
α-helix	384-396	13
α-helix	402-415	14
α-helix	422-434	13
α-helix	439-452	14
α-helix	460-469	10
α-helix	476-487	12
α-helix	494-507	14
α-helix	519-530	12
α-helix	535-551	17
α-helix	556-564	9
α-helix	566-569	4
α-helix	574-589	16
α-helix	593-598	6
α-helix	603-607	5
α-helix	613-619	7

Chain BBB: 40 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	16-21	6
α-helix	27-42	16
α-helix	47-50	4
α-helix	51-55	5
α-helix	63-76	14
α-helix	77-79	3
α-helix	83-87	5
α-helix	88-92	5
α-helix	100-110	11
α-helix	116-130	15
α-helix	135-148	14
α-helix	156-158	3
α-helix	162-167	6
α-helix	174-187	14
α-helix	201-210	10
α-helix	216-226	11
α-helix	234-244	11
α-helix	254-265	12
α-helix	277-283	7
α-helix	285-290	6
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	385-387	3
α-helix	388-400	13
α-helix	404-418	15
α-helix	427-433	7
α-helix	442-454	13
α-helix	462-468	7
α-helix	482-494	13
α-helix	496-498	3
α-helix	501-512	12
α-helix	517-532	16
α-helix	534-541	8
α-helix	547-549	3
α-helix	557-564	8
β-strand	569	1	2
α-helix	571-574	4
α-helix	578-580	3

Chain DDD: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	319	1	5
β-strand	323-324	2	5

Chain GGG: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	363-365	3
α-helix	374-383	10

Chain MMM: 10 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	3
β-strand	14-17	4	3
α-helix	26-32	7
α-helix	33-37	5
β-strand	49-50	2	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	105-115	11
β-strand	116-117	2	4
β-strand	120-121	2	4
α-helix	126-129	4
α-helix	145-156	12
β-strand	167-168	2	5
β-strand	176-185	10	6
β-strand	191-201	11	6
β-strand	211-215	5	7
β-strand	256-259	4	6
β-strand	263	1	8
α-helix	267-269	3
β-strand	275	1	7
β-strand	276	1	8
α-helix	278-279	2
β-strand	286-290	5	6
β-strand	298	1	9
β-strand	304	1	10
β-strand	311-319	9	10
β-strand	320	1	9
β-strand	327-336	10	11
β-strand	341	1	12
β-strand	345-348	4	10
β-strand	352-353	2	11
β-strand	361-370	10	11
β-strand	374-382	9	10
β-strand	383	1	12
β-strand	396-397	2	6
β-strand	398-402	5	11
β-strand	403	1	6
β-strand	414-418	5	7
α-helix	426-428	3
β-strand	434-438	5	6
β-strand	442-445	4	6

Chain SSS: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	13
β-strand	14-17	4	13
α-helix	26-39	14
β-strand	51-52	2	13
β-strand	54-61	8	13
β-strand	66-71	6	13
α-helix	78-94	17
α-helix	102-105	4
α-helix	111-117	7
β-strand	118-120	3	14
β-strand	122-123	2	14
α-helix	128-140	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-2 complex subunit alpha-2	AAA	protein	621	Rattus norvegicus	P18484 (AlphaFold model)
AP-2 complex subunit beta	BBB	protein	591	Homo sapiens	P63010 (AlphaFold model)
AP-2 complex subunit mu	CCC, MMM	protein	446	Rattus norvegicus	P84092 (AlphaFold model)
AP-2 complex subunit sigma	SSS	protein	142	Mus musculus	P62743 (AlphaFold model)
F-BAR domain only protein 2	DDD, GGG	protein	152	Homo sapiens	Q0JRZ9
TGN38 cargo peptide	PPP	protein	6	Homo sapiens

Sequence of entity 1 (AAA), FASTA

>7OG1_1 AP-2 complex subunit alpha-2 (chains AAA)
MPAVSKGEGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA
STDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKV
QHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSE
FSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSI
REEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAA
KTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRAL
LLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLE
EMPPFPERESSILAKLKKKKG

Sequence of entity 2 (BBB), FASTA

>7OG1_2 AP-2 complex subunit beta (chains BBB)
MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANA
VAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQY
VALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRK
YPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQV
QLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEV
VLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRK

Sequence of entity 3 (CCC, MMM), FASTA

>7OG1_3 AP-2 complex subunit mu (chains CCC, MMM)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLES
VNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSMEQK
LISEEDLGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRV
IPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASEN
AIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEP
KLNYSDHDVIKWVRYIGRSGIYETRC

Sequence of entity 4 (SSS), FASTA

>7OG1_4 AP-2 complex subunit sigma (chains SSS)
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYR
RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLMLQSLE

Sequence of entity 5 (DDD, GGG), FASTA

>7OG1_5 F-BAR domain only protein 2 (chains DDD, GGG)
GSPEFNIPDVDEEGYSIKPETNQNDTKENHFYSSSDSDSEDEEPKKYRIEIKPMHPNNSH
HTMASLDELKVSIGNITLSPAISRHSPVQMNRNLSNEELTKSKPSAPPNEKGTSDLLAWD
PLFGPSLDSSSSSSLTEFPGRPHHHHHHHHHH

Sequence of entity 6 (PPP), FASTA

>7OG1_6 TGN38 CARGO PEPTIDE (chains PPP)
DYQRLN

Primary citation

FCHO controls AP2's initiating role in endocytosis through a PtdIns(4,5)P 2 -dependent switch. Zaccai, N.R., Kadlecova, Z., Dickson, V.K. et al. Sci Adv (2022) 8:eabn2018-eabn2018. DOI 10.1126/sciadv.abn2018 · 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
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
6QH6 5.0 Å, AP2 clathrin adaptor core with two cargo peptides in open+ conformation

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