2JKT: Ap-2 complex subunit alpha-2

AP2 CLATHRIN ADAPTOR CORE with CD4 Dileucine peptide RM(phosphoS) EIKRLLSE Q to E mutant. Determined by X-ray diffraction at 3.4 Å resolution. Released 28 Oct 2008.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: MUS MUSCULUS, HOMO SAPIENS, RATTUS NORVEGICUS
Chains: 10
Atoms: 28,120
Mol. weight: 412.88 kDa
Released: 28 Oct 2008

Explore 2JKT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2JKT contains 191 α-helices and 78 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.

Chain A: 37 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	11-18	8
α-helix	28-40	13
α-helix	52-66	15
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	150-156	7
α-helix	162-178	17
α-helix	188-193	6
α-helix	194-197	4
α-helix	201-215	15
α-helix	225-236	12
β-strand	248-249	2	1
β-strand	252-253	2	1
α-helix	255-265	11
α-helix	274-292	19
α-helix	300-320	21
α-helix	324-339	16
α-helix	344-356	13
α-helix	365-369	5
α-helix	370-379	10
α-helix	383-394	12
α-helix	402-414	13
α-helix	418-435	18
α-helix	439-449	11
α-helix	454-456	3
α-helix	459-471	13
α-helix	476-486	11
α-helix	494-506	13
α-helix	515-517	3
α-helix	519-530	12
α-helix	535-551	17
α-helix	556-560	5
α-helix	566-569	4
α-helix	574-588	15
α-helix	592-598	7
α-helix	604-606	3
β-strand	611-614	4	2

Chains B and E: 42 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	15-23	9
α-helix	27-39	13
α-helix	51-55	5
α-helix	63-74	12
α-helix	85-87	3
α-helix	88-94	7
α-helix	100-110	11
α-helix	116-119	4
α-helix	123-129	7
α-helix	135-149	15
α-helix	153-158	6
α-helix	161-168	8
α-helix	174-190	17
α-helix	203-210	8
α-helix	219-226	8
α-helix	234-244	11
α-helix	245-247	3
α-helix	253-266	14
α-helix	274-289	16
α-helix	296-312	17
α-helix	314-317	4
α-helix	319-324	6
α-helix	326-327	2
α-helix	332-345	14
α-helix	351-363	13
α-helix	367-383	17
α-helix	385-387	3
α-helix	388-399	12
α-helix	404-418	15
α-helix	426-432	7
α-helix	442-453	12
α-helix	456-458	3
α-helix	462-470	9
α-helix	478-494	17
α-helix	500-508	9
α-helix	509-513	5
α-helix	517-532	16
α-helix	534-541	8
α-helix	547-549	3
α-helix	557-564	8
β-strand	569	1	3
α-helix	570-572	3
α-helix	578-580	3

Chains I and S: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	5
β-strand	14-19	6	5
α-helix	25-39	15
β-strand	49-52	4	5
β-strand	55-62	8	5
β-strand	65-71	7	5
α-helix	77-91	15
α-helix	92-96	5
β-strand	99	1	6
α-helix	102-105	4
α-helix	107-117	11
β-strand	118-119	2	7
β-strand	122-123	2	7
α-helix	128-135	8

Chain L: 36 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
α-helix	28-40	13
α-helix	52-66	15
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	150-156	7
α-helix	162-178	17
α-helix	188-193	6
α-helix	194-197	4
α-helix	201-214	14
α-helix	225-238	14
β-strand	248-249	2	8
β-strand	252-253	2	8
α-helix	255-265	11
α-helix	274-292	19
α-helix	300-320	21
α-helix	324-339	16
α-helix	344-356	13
α-helix	365-369	5
α-helix	370-379	10
α-helix	383-394	12
α-helix	402-414	13
α-helix	418-435	18
α-helix	439-449	11
α-helix	454-456	3
α-helix	459-471	13
α-helix	476-486	11
α-helix	494-506	13
α-helix	515-517	3
α-helix	519-530	12
α-helix	535-551	17
α-helix	556-560	5
α-helix	566-569	4
α-helix	574-588	15
α-helix	592-598	7
β-strand	611-614	4	9

Chains M and U: 11 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	10
β-strand	14-19	6	10
α-helix	27-32	6
α-helix	33-37	5
β-strand	47-49	3	10
β-strand	54-59	6	10
β-strand	64-69	6	10
β-strand	74	1	3
α-helix	75-93	19
α-helix	98-102	5
α-helix	105-115	11
β-strand	116-117	2	11
β-strand	120-121	2	11
α-helix	129-131	3
β-strand	171-185	15	12
β-strand	191-197	7	12
β-strand	200-205	6	12
β-strand	211-216	6	13
β-strand	245-248	4	12
β-strand	252-253	2	13
α-helix	254-256	3
β-strand	263-265	3	13
α-helix	267-268	2
β-strand	270-279	10	12
β-strand	287-292	6	2
β-strand	302-309	8	2
β-strand	316-325	10	12
α-helix	326-327	2
β-strand	330-335	6	2
β-strand	341-345	5	12
α-helix	346-348	3
β-strand	350-359	10	12
β-strand	363-372	10	2
β-strand	386-392	7	12
β-strand	401-407	7	13
α-helix	415-417	3
β-strand	418-433	16	12

Chains P and Q: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ap-2 complex subunit alpha-2	A, L	protein	623	MUS MUSCULUS	P17427 (AlphaFold model)
Ap-2 complex subunit beta-1	B, E	protein	591	HOMO SAPIENS	P63010 (AlphaFold model)
Ap-2 complex subunit sigma-1	I, S	protein	142	MUS MUSCULUS	P62743 (AlphaFold model)
Ap-2 complex subunit mu-1	M, U	protein	435	RATTUS NORVEGICUS	P84092 (AlphaFold model)
CD4 peptide	P, Q	protein	11	HOMO SAPIENS	P01730

Sequence of entity 1 (A, L), FASTA

>2JKT_1 AP-2 COMPLEX SUBUNIT ALPHA-2 (chains A, L)
MPAVSKGDGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA
STDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKV
QHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSE
FSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSI
REEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAA
KTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRAL
LLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLE
EMPPFPERESSILAKLKKKKGGS

Sequence of entity 2 (B, E), FASTA

>2JKT_2 AP-2 COMPLEX SUBUNIT BETA-1 (chains B, E)
MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANA
VAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQY
VALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRK
YPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQV
QLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEV
VLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRK

Sequence of entity 3 (I, S), FASTA

>2JKT_3 AP-2 COMPLEX SUBUNIT SIGMA-1 (chains I, S)
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYR
RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLMLQSLE

Sequence of entity 4 (M, U), FASTA

>2JKT_4 AP-2 COMPLEX SUBUNIT MU-1 (chains M, U)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLES
VNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQS
IAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTK
LEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAG
MKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIK
WVRYIGRSGIYETRC

Sequence of entity 5 (P, Q), FASTA

>2JKT_5 CD4 PEPTIDE (chains P, Q)
RMSEIKRLLSE

Primary citation

A Structural Explanation for the Binding of Endocytic Dileucine Motifs by the Ap2 Complex. Kelly, B.T., Mccoy, A.J., Spaete, K. et al. Nature (2008) 456:976. DOI 10.1038/NATURE07422 · 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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