6OXL: Phosphorylated ap-2

cryo-EM structure of phosphorylated ap-2 (mu E302K) bound to necap in the presence of ss DNA. Determined by electron microscopy at 3.5 Å resolution. Released 11 Sept 2019.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Mus musculus, Rattus norvegicus
Chains: 6
Atoms: 14,413
Mol. weight: 232.7 kDa
Released: 11 Sept 2019

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

Secondary structure: helices and β-sheets

6OXL contains 105 α-helices and 47 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: 42 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
α-helix	27-44	18
α-helix	53-67	15
α-helix	76-83	8
α-helix	88-100	13
α-helix	106-120	15
α-helix	125-138	14
α-helix	141-147	7
α-helix	151-156	6
α-helix	162-178	17
α-helix	189-192	4
α-helix	193-197	5
α-helix	202-217	16
α-helix	223-225	3
α-helix	226-237	12
β-strand	248-249	2	1
β-strand	252-253	2	1
α-helix	257-263	7
α-helix	265-267	3
α-helix	274-290	17
α-helix	294-295	2
α-helix	300-303	4
α-helix	305-320	16
α-helix	324-334	11
α-helix	337-339	3
α-helix	343-356	14
α-helix	363-366	4
α-helix	367-369	3
α-helix	370-379	10
α-helix	383-396	14
α-helix	399-401	3
α-helix	402-413	12
α-helix	421-434	14
α-helix	439-453	15
α-helix	459-471	13
α-helix	476-486	11
α-helix	494-506	13
α-helix	508-510	3
α-helix	519-528	10
α-helix	535-551	17
α-helix	556-563	8
α-helix	574-588	15
α-helix	593-598	6
α-helix	600-603	4

Chain B: 49 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	14-22	9
α-helix	27-43	17
α-helix	48-50	3
α-helix	51-54	4
α-helix	55-58	4
α-helix	63-78	16
α-helix	81-84	4
α-helix	85-87	3
α-helix	88-91	4
α-helix	101-112	12
α-helix	116-118	3
α-helix	119-129	11
α-helix	137-150	14
α-helix	162-169	8
α-helix	176-186	11
α-helix	187-189	3
α-helix	203-211	9
α-helix	218-221	4
α-helix	223-226	4
α-helix	236-244	9
α-helix	245-248	4
α-helix	253-263	11
α-helix	276-279	4
α-helix	280-282	3
α-helix	285-289	5
α-helix	296-312	17
α-helix	325-327	3
α-helix	332-344	13
α-helix	351-362	12
α-helix	367-373	7
α-helix	375-381	7
α-helix	385-387	3
α-helix	388-398	11
α-helix	399-401	3
α-helix	407-420	14
α-helix	426-428	3
α-helix	429-432	4
α-helix	433-435	3
α-helix	442-453	12
α-helix	462-465	4
α-helix	478-494	17
α-helix	500-506	7
α-helix	517-530	14
α-helix	534-540	7
α-helix	545-547	3
α-helix	557-563	7
α-helix	564-566	3
β-strand	569	1	2
α-helix	570-573	4
α-helix	578-580	3

Chain M: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	3
β-strand	14-17	4	3
α-helix	27-32	6
α-helix	33-37	5
β-strand	47-49	3	3
β-strand	54-59	6	3
β-strand	64-69	6	3
β-strand	74	1	2
α-helix	75-93	19
α-helix	98-102	5
α-helix	105-111	7
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	191-204	14	5
β-strand	211-216	6	6
β-strand	245-248	4	5
β-strand	253	1	6
β-strand	262-265	4	6
α-helix	267-268	2
β-strand	270	1	5
β-strand	273-279	7	5
β-strand	287-296	10	7
β-strand	300-309	10	7
β-strand	316-325	10	5
β-strand	330-336	7	7
β-strand	341-345	5	5
β-strand	350-359	10	5
β-strand	363-372	10	7
β-strand	386-392	7	5
β-strand	401-407	7	6
β-strand	419-422	4	5
β-strand	425-433	9	5

Chain N: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	8-19	12	10
α-helix	32-34	3
β-strand	42-51	10	10
β-strand	54-60	7	10
β-strand	67-72	6	10
β-strand	81-83	3	11
β-strand	90	1	10
β-strand	91-96	6	11
β-strand	102-105	4	11
β-strand	106-109	4	10
α-helix	113-137	25

Chain S: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	8
β-strand	14-19	6	8
α-helix	25-35	11
β-strand	49-50	2	8
β-strand	56-58	3	8
β-strand	61-62	2	8
β-strand	65-71	7	8
α-helix	79-95	17
α-helix	100-103	4
α-helix	107-117	11
β-strand	118-119	2	9
β-strand	122-123	2	9
α-helix	128-139	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-2 complex subunit alpha-2	A	protein	621	Mus musculus	P17427 (AlphaFold model)
AP-2 complex subunit beta	B	protein	591	Mus musculus	Q9DBG3 (AlphaFold model)
AP-2 complex subunit mu	M	protein	435	Mus musculus	P84091 (AlphaFold model)
AP-2 complex subunit sigma	S	protein	142	Rattus norvegicus	P62744 (AlphaFold model)
Adaptin ear-binding coat-associated protein 2	N	protein	266	Mus musculus	Q9D1J1
Unknown region of Adaptin ear-binding coat-associated protein 2 Ex-domain	n	protein	7	Mus musculus

Sequence of entity 1 (A), FASTA

>6OXL_1 AP-2 complex subunit alpha-2 (chains A)
MPAVSKGEGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKYVC
KLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKNDL
ASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRTSP
DLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVTSA
STDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSKKV
QHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLASSE
FSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIVAEMLSYLETADYSI
REEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVIQIVINRDDVQGYAA
KTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLLHSKFHLCSVPTRAL
LLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRLSTVASTDILATVLE
EMPPFPERESSILAKLKKKKG

Sequence of entity 2 (B), FASTA

>6OXL_2 AP-2 complex subunit beta (chains B)
MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQT
DNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITE
YLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANA
VAALSEISESHPNSNLLDLNPQNINKLLTALNECTEWGQIFILDCLSNYNPKDDREAQSI
CERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNMLLKKLAPPLVTLLSGEPEVQY
VALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQANIAQVLAELKE
YATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFRK
YPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQV
QLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEV
VLSEKPLISEETDLIEPTLLDELICHIGSLASVYHKPPNAFVEGSHGIHRK

Sequence of entity 3 (M), FASTA

>6OXL_3 AP-2 complex subunit mu (chains M)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLES
VNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQS
IAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTK
LKVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAG
MKESQISAEIELLPTNDKKKWARPPISMNFEVPFAPSGLKVRYLKVFEPKLNYSDHDVIK
WVRYIGRSGIYETRC

Sequence of entity 4 (S), FASTA

>6OXL_4 AP-2 complex subunit sigma (chains S)
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYR
RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLMLQSLE

Sequence of entity 5 (N), FASTA

>6OXL_5 Adaptin ear-binding coat-associated protein 2 (chains N)
MEESEYESVLCVKPEVHVYRIPPRATNRGYRASEWQLDQPSWSGRLRITAKGKVAYIKLE
DRTSGELFAQAPVDQFPGTAVESVTDSSRYFVIRIEDGNGRRAFIGLGFGDRGDAFDFNV
ALQDHFKWVKQQCEFAKQAQNPDEGPKLDLGFKDGQTIKINIANMRKKEGAAGTPRARPT
SAGGLSLLPPPPGGKSSTVIPPSGEQLSVGGSLVQPAVVSGSGGATELWPQSKPAAAATA
DIWGDFTKSTGSPSSQSQPGTGWVQF

Sequence of entity 6 (n), FASTA

>6OXL_6 Unknown region of Adaptin ear-binding coat-associated protein 2 Ex-domain (chains n)
XXXXXXX

Primary citation

A structural mechanism for phosphorylation-dependent inactivation of the AP2 complex. Partlow, E.A., Baker, R.W., Beacham, G.M. et al. Elife (2019) 8. DOI 10.7554/eLife.50003 · 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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