7RWA: AP2

AP2 bound to heparin and Tgn38 tyrosine cargo peptide. Determined by electron microscopy at 4.7 Å resolution. Released 30 Mar 2022.

Method: Electron microscopy
Resolution: 4.7 Å
Organism: Mus musculus
Chains: 10
Atoms: 16,158
Mol. weight: 412.2 kDa
Released: 30 Mar 2022

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

Secondary structure: helices and β-sheets

7RWA contains 174 α-helices and 80 β-strands across 10 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.

Chains a and A: 41 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
α-helix	26-44	19
α-helix	53-68	16
α-helix	77-83	7
α-helix	88-100	13
α-helix	107-120	14
α-helix	125-137	13
α-helix	141-145	5
α-helix	150-155	6
α-helix	162-178	17
α-helix	189-192	4
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	11
β-strand	252-253	2	11
α-helix	255-265	11
α-helix	269	1
α-helix	271	1
α-helix	274-292	19
α-helix	294-295	2
α-helix	300-320	21
α-helix	324-338	15
α-helix	343-356	14
α-helix	360-368	9
α-helix	370-379	10
α-helix	384-395	12
α-helix	399-414	16
α-helix	420-434	15
α-helix	439-452	14
α-helix	461-472	12
α-helix	475-487	13
α-helix	494-511	18
α-helix	515-517	3
α-helix	519-529	11
α-helix	535-551	17
α-helix	556-562	7
α-helix	566-569	4
α-helix	574-589	16
α-helix	594-598	5
α-helix	603-607	5

Chains b and B: 31 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	88-95	8
α-helix	100-112	13
α-helix	118-130	13
α-helix	135-149	15
α-helix	156-167	12
α-helix	174-187	14
α-helix	201-213	13
α-helix	216-225	10
α-helix	226-228	3
α-helix	234-244	11
α-helix	253-265	13
α-helix	276-290	15
α-helix	291-293	3
α-helix	296-312	17
α-helix	325-327	3
α-helix	332-345	14
α-helix	351-362	12
α-helix	367-383	17
α-helix	385-399	15
α-helix	404-420	17
α-helix	428-434	7
α-helix	442-454	13
α-helix	462-469	8
α-helix	478-494	17
α-helix	496-498	3
α-helix	500-513	14
α-helix	517-530	14
α-helix	534-540	7
α-helix	557-563	7
β-strand	569	1	12
α-helix	570-574	5
α-helix	578-580	3

Chains m and M: 10 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	13
β-strand	14-19	6	13
α-helix	26-32	7
α-helix	33-37	5
β-strand	47-49	3	13
β-strand	54-60	7	13
β-strand	63-69	7	13
β-strand	74	1	12
α-helix	75-93	19
α-helix	98-102	5
α-helix	105-115	11
β-strand	116-117	2	14
β-strand	120-121	2	14
β-strand	171-185	15	15
β-strand	191-205	15	15
β-strand	211-216	6	16
β-strand	245-248	4	15
β-strand	253	1	16
β-strand	263-265	3	16
α-helix	267-268	2
β-strand	270-272	3	15
β-strand	275-279	5	15
α-helix	283-285	3
β-strand	287-290	4	17
β-strand	293-296	4	17
β-strand	300-309	10	17
β-strand	316	1	18
β-strand	318-325	8	15
β-strand	330-337	8	17
β-strand	341-345	5	15
β-strand	350-355	6	15
β-strand	359	1	18
β-strand	363-372	10	17
α-helix	373-374	2
α-helix	383-385	3
β-strand	386-392	7	15
β-strand	401-407	7	16
α-helix	415-417	3
β-strand	418-433	16	15

Chains s and S: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	19
β-strand	14-19	6	19
α-helix	25-40	16
β-strand	50-52	3	19
β-strand	55-62	8	19
β-strand	65-71	7	19
α-helix	77-95	19
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	20
β-strand	122-123	2	20
α-helix	128-140	13

Chains y and Y: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	350-352	3	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-2 complex subunit alpha-2	A, a	protein	630	Mus musculus	P17427 (AlphaFold model)
AP-2 complex subunit beta	B, b	protein	591	Mus musculus	Q9DBG3 (AlphaFold model)
AP-2 complex subunit mu	M, m	protein	435	Mus musculus	P84091 (AlphaFold model)
AP-2 complex subunit sigma	S, s	protein	142	Mus musculus	P62743 (AlphaFold model)
Trans-Golgi network integral membrane protein TGN38 peptide	Y, y	protein	15	Mus musculus	Q62314

Sequence of entity 1 (A, a), FASTA

>7RWA_1 AP-2 complex subunit alpha-2 (chains A, a)
MPAVSKGDGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA
STDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKV
QHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSE
FSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSI
REEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAA
KTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRAL
LLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLE
EMPPFPERESSILAKLKKKKGGSGLEVLFQ

Sequence of entity 2 (B, b), FASTA

>7RWA_2 AP-2 complex subunit beta (chains B, b)
MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANA
VAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQY
VALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRK
YPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQV
QLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEV
VLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRK

Sequence of entity 3 (M, m), FASTA

>7RWA_3 AP-2 complex subunit mu (chains M, m)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLES
VNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQS
IAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTK
LEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAG
MKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIK
WVRYIGRSGIYETRC

Sequence of entity 4 (S, s), FASTA

>7RWA_4 AP-2 complex subunit sigma (chains S, s)
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYR
RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLMLQSLE

Sequence of entity 5 (Y, y), FASTA

>7RWA_5 Trans-Golgi network integral membrane protein TGN38 peptide (chains Y, y)
CKVTRRPKAADYQRL

Primary citation

Structural basis of an endocytic checkpoint that primes the AP2 clathrin adaptor for cargo internalization. Partlow, E.A., Cannon, K.S., Hollopeter, G. et al. Nat Struct Mol Biol (2022) 29:339-347. DOI 10.1038/s41594-022-00749-z · 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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