6QH7: AP-2 complex subunit alpha

AP2 clathrin adaptor mu2T156-phosphorylated core with two cargo peptides in open+ conformation. Determined by X-ray diffraction at 3.4 Å resolution. Released 4 Sept 2019.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: Rattus norvegicus, Homo sapiens
Chains: 7
Atoms: 13,342
Mol. weight: 257.98 kDa
Released: 4 Sept 2019

Explore 6QH7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QH7 contains 92 α-helices and 37 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 A: 42 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	13-21	9
α-helix	26-44	19
α-helix	52-68	17
α-helix	76-82	7
α-helix	88-100	13
α-helix	106-121	16
α-helix	125-138	14
α-helix	141-147	7
α-helix	150-155	6
α-helix	162-178	17
α-helix	180-182	3
α-helix	189-194	6
α-helix	195-197	3
α-helix	201-215	15
α-helix	225-238	14
α-helix	245-247	3
β-strand	248	1	1
β-strand	253	1	1
α-helix	255-266	12
α-helix	274-292	19
α-helix	294-295	2
α-helix	300-320	21
α-helix	324-337	14
α-helix	343-356	14
α-helix	360-368	9
α-helix	370-379	10
α-helix	384-396	13
α-helix	399-415	17
α-helix	418-434	17
α-helix	439-452	14
α-helix	459-472	14
α-helix	475-487	13
α-helix	494-507	14
α-helix	508-511	4
α-helix	515-517	3
α-helix	519-528	10
α-helix	535-551	17
α-helix	553-555	3
α-helix	556-564	9
α-helix	566-569	4
α-helix	574-588	15
α-helix	592-598	7
α-helix	603-607	5
α-helix	611-618	8

Chain B: 37 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	85-87	3
α-helix	88-93	6
α-helix	101-103	3
α-helix	104-110	7
α-helix	119-129	11
α-helix	135-148	14
α-helix	156-166	11
α-helix	174-187	14
α-helix	201-213	13
α-helix	216-226	11
α-helix	234-244	11
α-helix	254-265	12
α-helix	277-289	13
α-helix	290-293	4
α-helix	296-312	17
α-helix	320-323	4
α-helix	326-327	2
α-helix	332-345	14
α-helix	351-361	11
α-helix	367-383	17
α-helix	387-399	13
α-helix	404-420	17
α-helix	426-428	3
α-helix	429-434	6
α-helix	435-438	4
α-helix	442-454	13
α-helix	462-470	9
α-helix	478-494	17
α-helix	496-498	3
α-helix	500-508	9
α-helix	509-513	5
α-helix	517-532	16
α-helix	534-541	8
α-helix	543-545	3
α-helix	557-565	9
β-strand	569	1	2
α-helix	570-574	5
α-helix	578-580	3

Chain M: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	172-185	14	3
β-strand	191-205	15	3
β-strand	211-216	6	4
β-strand	256-259	4	3
β-strand	274-276	3	4
α-helix	278-279	2
β-strand	281-290	10	3
β-strand	298-301	4	5
β-strand	304-307	4	5
β-strand	311-320	10	5
β-strand	327-336	10	3
α-helix	337-338	2
β-strand	343-348	6	5
β-strand	352-356	5	3
β-strand	361-370	10	3
β-strand	374-382	9	5
α-helix	395-397	3
β-strand	398-403	6	3
β-strand	412-418	7	4
β-strand	430-438	9	3
β-strand	442	1	3

Chain N: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	6
β-strand	14-18	5	6
α-helix	28-32	5
α-helix	33-37	5
β-strand	48-50	3	6
β-strand	53-60	8	6
β-strand	63-69	7	6
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	7
β-strand	120-121	2	7

Chain P: 0 helices, 1 β-strand

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

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	25-40	16
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	128-136	9

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)
Adaptor-related protein complex 2, mu 2 subunit, C-terminal domain	M, N	protein	446	Rattus norvegicus	P84092 (AlphaFold model)
TGN38 cargo peptide	P	protein	6	Homo sapiens
CD4 cargo peptide	Q	protein	10	Homo sapiens	P01730 (AlphaFold model)
AP-2 complex subunit sigma	S	protein	142	Rattus norvegicus	P62744

Sequence of entity 1 (A), FASTA

>6QH7_1 AP-2 complex subunit alpha (chains A)
MPAVSKGDGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA
STDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKV
QHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSE
FSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSI
REEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAA
KTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRAL
LLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLE
EMPPFPERESSILAKLKKKKG

Sequence of entity 2 (B), FASTA

>6QH7_2 AP-2 complex subunit beta (chains B)
MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANA
VAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQY
VALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRK
YPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQV
QLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEV
VLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRKH

Sequence of entity 3 (M, N), FASTA

>6QH7_3 ADAPTOR-RELATED PROTEIN COMPLEX 2, MU 2 SUBUNIT, C-TERMINAL DOMAIN (chains M, N)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLES
VNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSMEQK
LISEEDLGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRV
IPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASEN
AIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEP
KLNYSDHDVIKWVRYIGRSGIYETRC

Sequence of entity 4 (P), FASTA

>6QH7_4 TGN38 CARGO PEPTIDE (chains P)
DYQRLN

Sequence of entity 5 (Q), FASTA

>6QH7_5 CD4 CARGO PEPTIDE (chains Q)
RMSQIKRLLS

Sequence of entity 6 (S), FASTA

>6QH7_6 AP-2 complex subunit sigma (chains S)
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYR
RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLMLQSLE

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:

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
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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