7OHO: AP2 FCHO2 chimera

Name: PDB 7OHO: Crystal structure of AP2 FCHO2 chimera
Published: 2022-06-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: endocytosis

Crystal structure of AP2 FCHO2 chimera. Determined by X-ray diffraction at 2.88 Å resolution. Released 1 Jun 2022.

Method: X-ray diffraction
Resolution: 2.88 Å
Organisms: Rattus norvegicus, Homo sapiens, Mus musculus
Chains: 4
Atoms: 13,681
Mol. weight: 210.63 kDa
Ligands: IHP
Released: 1 Jun 2022

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

Secondary structure: helices and β-sheets

7OHO contains 96 α-helices and 35 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 AAA: 45 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-22	12
α-helix	26-45	20
α-helix	52-68	17
α-helix	76-81	6
α-helix	82-84	3
α-helix	88-100	13
α-helix	106-120	15
α-helix	125-138	14
α-helix	141-147	7
α-helix	150-156	7
α-helix	162-178	17
α-helix	180-182	3
α-helix	189-194	6
α-helix	195-197	3
α-helix	201-217	17
α-helix	219-222	4
α-helix	225-237	13
α-helix	245-247	3
β-strand	248-249	2	1
β-strand	252-253	2	1
α-helix	255-264	10
α-helix	265-267	3
α-helix	274-290	17
α-helix	300-320	21
α-helix	324-335	12
α-helix	343-356	14
α-helix	360-367	8
α-helix	370-379	10
α-helix	383-396	14
α-helix	402-415	14
α-helix	418-420	3
α-helix	421-434	14
α-helix	439-453	15
α-helix	454-456	3
α-helix	459-471	13
α-helix	473-475	3
α-helix	476-487	12
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	556-564	9
α-helix	566-569	4
α-helix	574-589	16
α-helix	592-598	7
α-helix	601-606	6

Chain BBB: 36 helices, 0 β-strands

Element	Residues	Length
α-helix	14-21	8
α-helix	27-42	16
α-helix	47-50	4
α-helix	51-56	6
α-helix	63-79	17
α-helix	81-84	4
α-helix	85-87	3
α-helix	88-96	9
α-helix	100-111	12
α-helix	119-130	12
α-helix	135-149	15
α-helix	158-169	12
α-helix	174-188	15
α-helix	201-213	13
α-helix	216-226	11
α-helix	234-244	11
α-helix	253-268	16
α-helix	277-283	7
α-helix	285-291	7
α-helix	296-312	17
α-helix	314-317	4
α-helix	321-324	4
α-helix	332-343	12
α-helix	351-362	12
α-helix	367-382	16
α-helix	388-398	11
α-helix	404-420	17
α-helix	429-432	4
α-helix	433-438	6
α-helix	442-453	12
α-helix	463-470	8
α-helix	478-492	15
α-helix	500-511	12
α-helix	517-532	16
α-helix	536-541	6
α-helix	560-566	7

Chain MMM: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	2
β-strand	14-19	6	2
α-helix	26-32	7
α-helix	33-37	5
β-strand	47	1	2
β-strand	50	1	3
β-strand	53	1	3
β-strand	54-60	7	2
β-strand	63-69	7	2
α-helix	75-93	19
α-helix	98-103	6
α-helix	105-112	8
β-strand	116-117	2	4
β-strand	120-121	2	4
α-helix	126-129	4
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	252-254	3	6
β-strand	263-265	3	6
α-helix	267-268	2
β-strand	270-279	10	5
β-strand	287-296	10	7
β-strand	300-309	10	7
β-strand	316-325	10	5
β-strand	330-337	8	7
β-strand	341-345	5	5
α-helix	346-348	3
β-strand	350-359	10	5
β-strand	363-372	10	7
α-helix	383-385	3
β-strand	386-392	7	5
β-strand	401-407	7	6
α-helix	415-417	3
β-strand	419-433	15	5

Chain SSS: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	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	77-94	18
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-2	AAA	protein	621	Rattus norvegicus	P18484 (AlphaFold model)
AP-2 complex subunit beta,F-BAR domain only protein 2	BBB	protein	636	Homo sapiens	P63010 (AlphaFold model), Q0JRZ9 (AlphaFold model)
AP-2 complex subunit mu	MMM	protein	446	Rattus norvegicus	P84092 (AlphaFold model)
AP-2 complex subunit sigma	SSS	protein	142	Mus musculus	P62743

Sequence of entity 1 (AAA), FASTA

>7OHO_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

>7OHO_2 AP-2 complex subunit beta,F-BAR domain only protein 2 (chains BBB)
MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANA
VAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQY
VALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRK
YPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQV
QLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEV
VLEIKPMHPNNSHHTMASLDELKVSIGNITLSPAISRHSPVQMNRNLSNEELTKSKPSAP
PNEKGTSDLLAWDPLFGPSLDSSSSFSLTGHHHHHH

Sequence of entity 3 (MMM), FASTA

>7OHO_3 AP-2 complex subunit mu (chains MMM)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLES
VNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSMEQK
LISEEDLGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRV
IPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASEN
AIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEP
KLNYSDHDVIKWVRYIGRSGIYETRC

Sequence of entity 4 (SSS), FASTA

>7OHO_4 AP-2 complex subunit sigma (chains SSS)
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYR
RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLMLQSLE

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	1

Water and common crystallization additives (GOL) are not listed.

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
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
6QH6 5.0 Å, AP2 clathrin adaptor core with two cargo peptides in open+ conformation

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