4EN2: HIV-1 Nef

HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain). Determined by X-ray diffraction at 2.58 Å resolution. Released 20 Jun 2012.

Method: X-ray diffraction
Resolution: 2.58 Å
Organisms: Mus musculus, Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 6,783
Mol. weight: 113.52 kDa
Released: 20 Jun 2012

Explore 4EN2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4EN2 contains 29 α-helices and 73 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: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	164	1	18
β-strand	169-183	15	14
β-strand	189-203	15	14
β-strand	206	1	18
β-strand	209-214	6	19
β-strand	216	1	20
α-helix	217-222	6
β-strand	231	1	20
β-strand	234-238	5	14
β-strand	242	1	19
α-helix	244-250	7
β-strand	253-255	3	19
α-helix	257-258	2
β-strand	260-269	10	14
β-strand	277-285	9	13
β-strand	290-299	10	13
β-strand	301	1	7
β-strand	306-315	10	14
β-strand	321-327	7	13
β-strand	331-335	5	14
β-strand	340-349	10	14
β-strand	353-361	9	13
α-helix	374-375	2
β-strand	376-383	8	14
β-strand	385-386	2	8
β-strand	392-398	7	19
β-strand	405-420	16	14

Chain B: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-22	16
β-strand	66	1	7
β-strand	68-69	2	8
β-strand	76	1	9
β-strand	77	1	10
α-helix	78-80	3
α-helix	81-94	14
α-helix	100	1
β-strand	101	1	11
α-helix	102	1
α-helix	104-118	15
β-strand	120	1	10
β-strand	127	1	12
β-strand	134	1	11
β-strand	136	1	12
β-strand	143-147	5	11
α-helix	150-158	9
β-strand	181-185	5	11
α-helix	187-190	4
α-helix	194-198	5
α-helix	200-202	3

Chain C: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-22	11
β-strand	58-59	2	13
β-strand	61-62	2	14
β-strand	66	1	5
β-strand	68-69	2	6
β-strand	77	1	15
α-helix	78-80	3
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
β-strand	181-185	5	16
α-helix	187-190	4
α-helix	194-198	5
α-helix	200-202	3

Chain D: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	321-322	2	1
β-strand	324	1	2

Chain E: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	321-322	2	14
β-strand	323	1	9
β-strand	324	1	19
α-helix	328-330	3

Chain M: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	169-183	15	1
β-strand	189-203	15	1
β-strand	209-214	6	2
β-strand	216	1	3
α-helix	217-222	6
β-strand	231	1	3
β-strand	234-238	5	1
β-strand	242	1	2
α-helix	244-250	7
β-strand	254-255	2	2
α-helix	257-258	2
β-strand	260-269	10	1
α-helix	273-275	3
β-strand	277-287	11	4
β-strand	290-299	10	4
β-strand	301	1	5
β-strand	306-315	10	1
β-strand	321-327	7	4
β-strand	331-335	5	1
β-strand	340-349	10	1
β-strand	353-361	9	4
α-helix	374-375	2
β-strand	376-383	8	1
β-strand	385-386	2	6
β-strand	392-398	7	2
β-strand	405-414	10	1
β-strand	418-420	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AP-1 complex subunit mu-1	A, M	protein	266	Mus musculus	P35585 (AlphaFold model)
Protein Nef	B, C	protein	206	Human immunodeficiency virus 1	Q90VU7
MHC-I	D, E	protein	28	Homo sapiens	P04439 (AlphaFold model)

Sequence of entity 1 (A, M), FASTA

>4EN2_1 AP-1 complex subunit mu-1 (chains A, M)
SWRSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDK
VLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLI
WIESVIEKHSHSRIEYMVKAKSQFKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPE
NSEIVWSVKSFPGGKEYLMRAHFGLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKI
IEKSGYQALPWVRYITQNGDYQLRTQ

Sequence of entity 2 (B, C), FASTA

>4EN2_2 Protein Nef (chains B, C)
MGGKWSKSSVIGWPAVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEA
QEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGY
FPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREV
LEWRFDSRLAFHHVARELHPEYFKNC

Sequence of entity 3 (D, E), FASTA

>4EN2_3 MHC-I (chains D, E)
DRKGGSYSQAAGSDSAQGSDVSLTACKV

Primary citation

Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef. Jia, X., Singh, R., Homann, S. et al. Nat Struct Mol Biol (2012) 19:701-706. DOI 10.1038/nsmb.2328 · PubMed

Other PDB entries of the same protein (UniProt P35585 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7R4H 2.34 Å, phospho-STING binding to adaptor protein complex-1
4EMZ 2.9 Å, HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1…
4P6Z 3.0 Å, Crystal structure of the human BST2 cytoplasmic domain and the HIV-1 Vpu cytoplasmic…
6CM9 3.73 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit
6DFF 3.9 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer
1W63 4.0 Å, AP1 clathrin adaptor core
6D83 4.27 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant…
6D84 6.72 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef (L164A, L165A) dileucine mutant dimer
6CRI 6.8 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer
4HMY 7.0 Å, Structural basis for recruitment and activation of the AP-1 clathrin adaptor complex by…
8D4E 9.2 Å, Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r)…
8D4C 9.3 Å, beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I…

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