6QH5: AP-2 complex subunit alpha

AP2 clathrin adaptor mu2T156-phosphorylated core in closed conformation. Determined by X-ray diffraction at 2.56 Å resolution. Released 4 Sept 2019.

Method: X-ray diffraction
Resolution: 2.56 Å
Organisms: Rattus norvegicus, Homo sapiens, Mus musculus
Chains: 5
Atoms: 13,770
Mol. weight: 256.61 kDa
Ligands: IHP
Released: 4 Sept 2019

Explore 6QH5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QH5 contains 98 α-helices and 33 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: 43 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-22	12
α-helix	26-43	18
α-helix	49-51	3
α-helix	52-67	16
α-helix	76-84	9
α-helix	88-100	13
α-helix	106-121	16
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	189-195	7
α-helix	201-217	17
α-helix	219-222	4
α-helix	225-237	13
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	294-295	2
α-helix	300-320	21
α-helix	324-337	14
α-helix	343-356	14
α-helix	360-367	8
α-helix	370-377	8
α-helix	383-395	13
α-helix	402-414	13
α-helix	421-435	15
α-helix	439-453	15
α-helix	454-456	3
α-helix	459-468	10
α-helix	476-487	12
α-helix	494-507	14
α-helix	509-512	4
α-helix	515-517	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	574-586	13
α-helix	593-598	6
α-helix	603-605	3

Chain B: 40 helices, 0 β-strands

Element	Residues	Length
α-helix	13-23	11
α-helix	27-41	15
α-helix	48-50	3
α-helix	51-55	5
α-helix	56-58	3
α-helix	63-79	17
α-helix	89-92	4
α-helix	93-95	3
α-helix	100-110	11
α-helix	119-122	4
α-helix	125-129	5
α-helix	135-150	16
α-helix	157-160	4
α-helix	162-169	8
α-helix	174-188	15
α-helix	200-213	14
α-helix	218-226	9
α-helix	236-243	8
α-helix	254-265	12
α-helix	277-290	14
α-helix	296-312	17
α-helix	321-324	4
α-helix	325-327	3
α-helix	332-344	13
α-helix	351-361	11
α-helix	367-383	17
α-helix	388-400	13
α-helix	404-420	17
α-helix	427-433	7
α-helix	436-438	3
α-helix	442-452	11
α-helix	462-470	9
α-helix	478-494	17
α-helix	500-511	12
α-helix	517-530	14
α-helix	536-542	7
α-helix	545-547	3
α-helix	559-564	6
α-helix	571-574	4
α-helix	578-580	3

Chain M: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	172-185	14	4
β-strand	191-205	15	4
β-strand	211-216	6	5
β-strand	245-248	4	4
β-strand	253-254	2	5
β-strand	262-265	4	5
α-helix	266-268	3
β-strand	270-279	10	4
β-strand	287-296	10	6
β-strand	300-309	10	6
β-strand	316-325	10	4
β-strand	330-337	8	6
β-strand	341-345	5	4
α-helix	346-348	3
β-strand	350-359	10	4
β-strand	363-372	10	6
α-helix	384-385	2
β-strand	386-392	7	4
β-strand	401-407	7	5
α-helix	415-417	3
β-strand	419-433	15	4

Chain N: 6 helices, 7 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	47-50	4	2
β-strand	53-60	8	2
β-strand	63-69	7	2
α-helix	75-93	19
α-helix	98-103	6
α-helix	105-115	11
β-strand	116-117	2	3
β-strand	120-121	2	3
α-helix	126-132	7

Chain S: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	7
β-strand	14-19	6	7
α-helix	25-39	15
β-strand	49-52	4	7
β-strand	55-62	8	7
β-strand	65-71	7	7
α-helix	77-94	18
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	8
β-strand	122-123	2	8
α-helix	128-140	13

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	592	Homo sapiens	P63010 (AlphaFold model)
AP-2 complex subunit mu	N	protein	446	Rattus norvegicus	P84092 (AlphaFold model)
AP-2 complex subunit mu	M	protein	446	Rattus norvegicus	P84092 (AlphaFold model)
AP-2 complex subunit sigma	S	protein	142	Mus musculus	P62743 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6QH5_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

>6QH5_2 AP-2 complex subunit beta (chains B)
MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANA
VAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQY
VALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRK
YPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQV
QLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEV
VLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRKH

Sequence of entity 3 (N), FASTA

>6QH5_3 AP-2 complex subunit mu (chains N)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLES
VNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSMEQK
LISEEDLGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRV
IPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASEN
AIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEP
KLNYSDHDVIKWVRYIGRSGIYETRC

Sequence of entity 4 (M), FASTA

>6QH5_4 AP-2 complex subunit mu (chains M)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLES
VNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSMEQK
LISEEDLGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRV
IPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASEN
AIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEP
KLNYSDHDVIKWVRYIGRSGIYETRC

Sequence of entity 5 (S), FASTA

>6QH5_5 AP-2 complex subunit sigma (chains S)
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYR
RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLMLQSLE

Ligands and cofactors

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

Primary citation

Temporal Ordering in Endocytic Clathrin-Coated Vesicle Formation via AP2 Phosphorylation. Wrobel, A.G., Kadlecova, Z., Kamenicky, J. et al. Dev Cell (2019) 50:494-508.e11. DOI 10.1016/j.devcel.2019.07.017 · PubMed

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

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

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