6URI: HIV-1 Nef

HIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 clathrin adaptor complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 29 Jul 2020.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Rattus norvegicus, Homo sapiens, Human immunodeficiency virus 1
Chains: 6
Atoms: 12,263
Mol. weight: 202.04 kDa
Released: 29 Jul 2020

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

Secondary structure: helices and β-sheets

6URI contains 101 α-helices and 28 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: 43 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	13-21	9
α-helix	26-46	21
α-helix	53-68	16
α-helix	76-83	8
α-helix	88-100	13
α-helix	107-120	14
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	189-193	5
α-helix	194-197	4
α-helix	201-217	17
α-helix	220-222	3
α-helix	224-238	15
β-strand	248	1	1
β-strand	253	1	1
α-helix	255-264	10
α-helix	265-267	3
α-helix	274-290	17
α-helix	294-295	2
α-helix	300-320	21
α-helix	324-337	14
α-helix	343-356	14
α-helix	363-367	5
α-helix	370-379	10
α-helix	383-395	13
α-helix	402-413	12
α-helix	418-420	3
α-helix	421-434	14
α-helix	439-452	14
α-helix	459-471	13
α-helix	473-475	3
α-helix	476-487	12
α-helix	494-507	14
α-helix	509-512	4
α-helix	519-527	9
α-helix	535-551	17
α-helix	556-563	8
α-helix	566-569	4
α-helix	574-588	15
α-helix	592-598	7
α-helix	600-607	8
α-helix	611-617	7

Chain B: 32 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	15-22	8
α-helix	92-94	3
α-helix	100-112	13
α-helix	125-131	7
α-helix	135-151	17
α-helix	168-170	3
α-helix	174-187	14
α-helix	207-213	7
α-helix	216-227	12
α-helix	234-242	9
α-helix	245-247	3
α-helix	253-266	14
α-helix	276-283	8
α-helix	285-290	6
α-helix	291-293	3
α-helix	296-312	17
α-helix	332-345	14
α-helix	350-361	12
α-helix	367-379	13
α-helix	380-382	3
α-helix	388-401	14
α-helix	404-420	17
α-helix	429-433	5
α-helix	442-454	13
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	557-564	8
β-strand	569	1	8
α-helix	570-574	5

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	412-417	6

Chain M: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	9
β-strand	14-19	6	9
α-helix	28-32	5
α-helix	33-37	5
β-strand	48-50	3	9
β-strand	53-60	8	9
β-strand	63-69	7	9
β-strand	74	1	8
α-helix	75-93	19
α-helix	98-103	6
α-helix	106-115	10
β-strand	116-117	2	10
β-strand	120-121	2	10

Chain N: 15 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	53-58	6
α-helix	63-66	4
α-helix	75-76	2
β-strand	77	1	5
α-helix	81-93	13
α-helix	100	1
β-strand	101	1	6
α-helix	102	1
α-helix	104-118	15
β-strand	120	1	5
β-strand	127	1	7
α-helix	133	1
β-strand	134	1	6
α-helix	135	1
β-strand	136	1	7
β-strand	143-147	5	6
α-helix	148-149	2
α-helix	150-156	7
β-strand	163	1	3
α-helix	167-169	3
β-strand	181-185	5	6
α-helix	188-191	4
α-helix	194-198	5
α-helix	200-202	3

Chain S: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	2
β-strand	14-19	6	2
α-helix	25-39	15
β-strand	49-52	4	2
β-strand	55-62	8	2
β-strand	65-71	7	2
α-helix	77-95	19
β-strand	99	1	3
α-helix	102-105	4
α-helix	107-117	11
β-strand	118-119	2	4
β-strand	122-123	2	4
α-helix	128-140	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-2 complex subunit alpha	A	protein	641	Rattus norvegicus	P18484 (AlphaFold model)
AP-2 complex subunit sigma	S	protein	142	Homo sapiens	P53680 (AlphaFold model)
Protein Nef	N	protein	186	Human immunodeficiency virus 1	P03406
AP-2 complex subunit beta	B	protein	615	Homo sapiens	P63010 (AlphaFold model)
AP-2 complex subunit mu	M	protein	135	Homo sapiens	Q96CW1
cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4	D	protein	62	Homo sapiens	P01730

Sequence of entity 1 (A), FASTA

>6URI_1 AP-2 complex subunit alpha (chains A)
MGSSHHHHHHSQDPMPAVSKGEGMRGLAVFISDIRNCKSKEAEIKRINKELANIRSKFKG
DKALDGYSKKKYVCKLLFIFLLGHDIDFGHMEAVNLLSSNRYTEKQIGYLFISVLVNSNS
ELIRLINNAIKNDLASRNPTFMGLALHCIANVGSREMAEAFAGEIPKILVAGDTMDSVKQ
SAALCLLRLYRTSPDLVPMGDWTSRVVHLLNDQHLGVVTAATSLITTLAQKNPEEFKTSV
SLAVSRLSRIVTSASTDLQDYTYYFVPAPWLSVKLLRLLQCYPPPEDPAVRGRLTECLET
ILNKAQEPPKSKKVQHSNAKNAVLFEAISLIIHHDSEPNLLVRACNQLGQFLQHRETNLR
YLALESMCTLASSEFSHEAVKTHIETVINALKTERDVSVRQRAVDLLYAMCDRSNAQQIV
AEMLSYLETADYSIREEIVLKVAILAEKYAVDYTWYVDTILNLIRIAGDYVSEEVWYRVI
QIVINRDDVQGYAAKTVFEALQAPACHENLVKVGGYILGEFGNLIAGDPRSSPLIQFNLL
HSKFHLCSVPTRALLLSTYIKFVNLFPEVKATIQDVLRSDSQLKNADVELQQRAVEYLRL
STVASTDILATVLEEMPPFPERESSILAKLKKKKGENLYFQ

Sequence of entity 2 (S), FASTA

>6URI_2 AP-2 complex subunit sigma (chains S)
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDARHTNFVEFRNFKIIYR
RYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLMLQSLE

Sequence of entity 3 (N), FASTA

>6URI_3 Protein Nef (chains N)
AGFSMAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEAQEEEEVGFPVTPQVPLRPMT
YKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFG
WCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHP
EYFKNC

Sequence of entity 4 (B), FASTA

>6URI_4 AP-2 complex subunit beta (chains B)
MGSSHHHHHHSQDPNSSSARLQVDMTDSKYFTTNKKGEISELKAELNNEKKEKRKEAVKK
VIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVYLYLMNYAKSQPDMAIMAVNSFVKDCE
DPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMV
EDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTALNECTE
WGQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDY
YNMLLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKL
EKLDIMIRLASQANIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLL
DLIQTKVNYVVQEAIVVIRDIFRKHPNKYESIIATLCGNLDSLDEPDARAAMIWIVGEYA
ERIDNADELLESFLEGFHDESTQVQLTLLTAIVKLFLKKPSETQELVQQVLSLATQDSDN
PDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPTLLDELICHIGSLASVYHK
PPNAFVEGSHGIHRK

Sequence of entity 5 (M), FASTA

>6URI_5 AP-2 complex subunit mu (chains M)
MIGGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQVRSPVTNIARTSFFHVKR
SNIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGY
PQNSETGALKTFITQ

Sequence of entity 6 (D), FASTA

>6URI_6 cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4 (chains D)
GVDGSDEASELACPTPKEDGLAQQQTQLNLRGSGSGCVRCRHRRRQAERMSQIKRLLSEK
KT

Primary citation

Structural basis of CD4 downregulation by HIV-1 Nef. Kwon, Y., Kaake, R.M., Echeverria, I. et al. Nat Struct Mol Biol (2020) 27:822-828. DOI 10.1038/s41594-020-0463-z · 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
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
6QH7 3.4 Å, AP2 clathrin adaptor mu2T156-phosphorylated core with two cargo peptides in open+…
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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