4NEE: AP-2 alpha/simga2 complex

crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef. Determined by X-ray diffraction at 2.88 Å resolution. Released 29 Jan 2014.

Method: X-ray diffraction
Resolution: 2.88 Å
Organisms: Rattus norvegicus, Human immunodeficiency virus 1
Chains: 12
Atoms: 21,530
Mol. weight: 316.4 kDa
Released: 29 Jan 2014

Explore 4NEE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NEE contains 172 α-helices and 70 β-strands across 12 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: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-21	11
α-helix	26-44	19
α-helix	52-67	16
α-helix	76-84	9
α-helix	88-100	13
α-helix	106-121	16
α-helix	127-138	12
α-helix	141-147	7
α-helix	150-156	7
α-helix	162-178	17
α-helix	188-195	8
α-helix	201-217	17
α-helix	220-222	3
α-helix	224-238	15
β-strand	248-249	2	14
β-strand	252-253	2	14
α-helix	255-265	11
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	363-367	5
α-helix	370-379	10
α-helix	383-395	13

Chain B: 28 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-22	12
α-helix	26-44	19
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	188-194	7
α-helix	195-197	3
α-helix	201-217	17
α-helix	219-222	4
α-helix	224-237	14
α-helix	245-247	3
β-strand	248-249	2	12
β-strand	252-253	2	12
α-helix	255-265	11
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	363-366	4
α-helix	367-369	3
α-helix	370-379	10
α-helix	383-395	13

Chain C: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	56-60	5
α-helix	75-76	2
α-helix	81-93	13
α-helix	100	1
β-strand	101	1	24
α-helix	102	1
α-helix	104-118	15
β-strand	127	1	25
β-strand	134	1	24
β-strand	136	1	25
β-strand	143-147	5	24
α-helix	148-149	2
α-helix	150-156	7
β-strand	163	1	2
β-strand	181-185	5	24
α-helix	188-191	4
α-helix	194-198	5
α-helix	200-202	3

Chain D: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
β-strand	14-19	6	1
α-helix	25-41	17
β-strand	49-51	3	1
β-strand	55-62	8	1
β-strand	65-72	8	1
α-helix	77-95	19
β-strand	99	1	2
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	3
β-strand	122-123	2	3
α-helix	128-140	13

Chain E: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	57-60	4
α-helix	75-76	2
β-strand	77	1	15
α-helix	81-94	14
α-helix	100	1
β-strand	101	1	16
α-helix	102	1
α-helix	104-118	15
β-strand	120	1	15
β-strand	127	1	17
β-strand	134	1	16
β-strand	136	1	17
β-strand	143-147	5	16
α-helix	148-149	2
α-helix	150-157	8
α-helix	167-170	4
β-strand	181-185	5	16
α-helix	188-191	4
α-helix	194-198	5
α-helix	200-202	3

Chain F: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	6
β-strand	14-19	6	6
α-helix	25-41	17
β-strand	49-51	3	6
β-strand	55-62	8	6
β-strand	65-72	8	6
α-helix	77-95	19
α-helix	100-105	6
α-helix	107-117	11
β-strand	118-119	2	7
β-strand	122-123	2	7
α-helix	128-140	13

Chain G: 27 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	11-22	12
α-helix	26-45	20
α-helix	49-51	3
α-helix	52-67	16
α-helix	76-83	8
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	201-217	17
α-helix	220-222	3
α-helix	224-238	15
α-helix	243-247	5
β-strand	248-249	2	11
β-strand	252-253	2	11
α-helix	255-265	11
α-helix	274-292	19
α-helix	294-295	2
α-helix	300-320	21
α-helix	324-338	15
α-helix	343-358	16
α-helix	363-366	4
α-helix	367-369	3
α-helix	370-379	10
α-helix	383-395	13

Chain H: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	57-64	8
β-strand	77	1	18
α-helix	81-93	13
α-helix	100	1
β-strand	101	1	19
α-helix	102	1
α-helix	104-118	15
β-strand	120	1	18
β-strand	127	1	20
β-strand	134	1	19
β-strand	136	1	20
β-strand	143-147	5	19
α-helix	148-149	2
α-helix	150-156	7
β-strand	163	1	9
α-helix	167-170	4
β-strand	181-185	5	19
α-helix	188-191	4
α-helix	194-198	5
α-helix	200-202	3

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-2 complex subunit sigma	D, F, I, L	protein	142	Rattus norvegicus	P62744 (AlphaFold model)
AP-2 complex subunit alpha-2	A, B, G, J	protein	398	Rattus norvegicus	P18484 (AlphaFold model)
Protein Nef	C, E, H, K	protein	155	Human immunodeficiency virus 1	P04601 (AlphaFold model)

Sequence of entity 1 (D, F, I, L), FASTA

>4NEE_1 AP-2 complex subunit sigma (chains D, F, I, L)
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYR
RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLMLQSLE

Sequence of entity 2 (A, B, G, J), FASTA

>4NEE_2 AP-2 complex subunit alpha-2 (chains A, B, G, J)
GAMPAVSKGEGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKGDKALDGYSKKKY
VCKLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNSELIRLINNAIKN
DLASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQSAALCLLRLYRT
SPDLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSVSLAVSRLSRIVT
SASTDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLETILNKAQEPPKSK
KVQHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLRYLALESMCTLAS
SEFSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAM

Sequence of entity 3 (C, E, H, K), FASTA

>4NEE_3 Protein Nef (chains C, E, H, K)
GXXXXXXXXXXXXXEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQD
ILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPV
SLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYF

Primary citation

How HIV-1 Nef hijacks the AP-2 clathrin adaptor to downregulate CD4. Ren, X., Park, S.Y., Bonifacino, J.S. et al. Elife (2014) 3:e01754-e01754. DOI 10.7554/eLife.01754 · PubMed

Other PDB entries of the same protein (UniProt P62744 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PWB 2.64 Å, Structure of AP-2 bound to the dileucine motif of CCDC32; combined map
6OWO 3.2 Å, cryo-EM structure of phosphorylated ap-2 core bound to necap
6QH7 3.4 Å, AP2 clathrin adaptor mu2T156-phosphorylated core with two cargo peptides in open+…
6OXL 3.5 Å, cryo-EM structure of phosphorylated ap-2 (mu E302K) bound to necap in the presence of ss…
6OWT 3.8 Å, Structure of SIVsmm Nef and SMM tetherin bound to the clathrin adaptor AP-2 complex

Browse structure collections

About this viewer

MolViewer shows 4NEE directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.