4EMZ: 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 2.9 Å resolution. Released 20 Jun 2012.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens, Mus musculus
Chains: 6
Atoms: 6,789
Mol. weight: 114.36 kDa
Released: 20 Jun 2012

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

Secondary structure: helices and β-sheets

4EMZ contains 32 α-helices and 74 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: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	164	1	17
β-strand	169-183	15	2
β-strand	189-191	3	2
β-strand	194-203	10	2
β-strand	206	1	17
β-strand	209-214	6	11
β-strand	216	1	18
α-helix	217-222	6
β-strand	231	1	18
β-strand	234-238	5	2
β-strand	242-243	2	11
α-helix	244-248	5
β-strand	254-255	2	11
α-helix	256-258	3
β-strand	260-269	10	2
α-helix	274-275	2
β-strand	277-285	9	1
β-strand	290-299	10	1
β-strand	301	1	12
β-strand	306-315	10	2
β-strand	321-327	7	1
β-strand	331-335	5	2
β-strand	340-349	10	2
β-strand	352-361	10	1
α-helix	374-375	2
β-strand	376-383	8	2
β-strand	385-386	2	13
β-strand	392-398	7	11
β-strand	405-420	16	2

Chain B: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	12-20	9
β-strand	66	1	12
β-strand	68-69	2	13
β-strand	77	1	14
α-helix	81-94	14
β-strand	101	1	15
α-helix	104-118	15
β-strand	120	1	14
β-strand	127	1	16
α-helix	133	1
β-strand	134	1	15
α-helix	135	1
β-strand	136	1	16
β-strand	143-147	5	15
β-strand	181-185	5	15
α-helix	187-190	4
α-helix	195-198	4
α-helix	200-202	3

Chain C: 13 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	13-20	8
β-strand	58-59	2	1
α-helix	61	1
β-strand	62	1	2
α-helix	63-64	2
β-strand	66	1	3
β-strand	68-69	2	4
β-strand	76	1	5
β-strand	77	1	6
α-helix	81-94	14
α-helix	100	1
β-strand	101	1	7
α-helix	102	1
α-helix	104-118	15
β-strand	120	1	6
β-strand	127	1	8
α-helix	133	1
β-strand	134	1	7
α-helix	135	1
β-strand	136	1	8
β-strand	143-147	5	7
β-strand	181-185	5	7
α-helix	187-190	4
α-helix	194-198	5
α-helix	200-202	3

Chain D: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	321-322	2	9
β-strand	323	1	5
β-strand	324	1	10

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	321-322	2	2
α-helix	323	1
β-strand	324	1	11

Chain M: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	169-183	15	9
β-strand	189-203	15	9
β-strand	209-214	6	10
β-strand	216	1	19
α-helix	217-222	6
β-strand	231	1	19
β-strand	234-238	5	9
β-strand	242-243	2	10
α-helix	244-250	7
β-strand	253-255	3	10
β-strand	260-270	11	9
β-strand	277-286	10	20
β-strand	290-299	10	20
β-strand	301	1	3
β-strand	306-315	10	9
β-strand	324-327	4	20
β-strand	331-335	5	9
α-helix	336-338	3
β-strand	340-349	10	9
β-strand	352-359	8	20
α-helix	374-375	2
β-strand	376-383	8	9
β-strand	385-386	2	4
β-strand	392-398	7	10
β-strand	405-414	10	9
β-strand	418-420	3	9

Molecules and chains

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

Sequence of entity 1 (B, C), FASTA

>4EMZ_1 Protein Nef (chains B, C)
MGGKWSKSSVIGWPAVRERMRRAEPAADGVGAVSRDLEKHGAITSSNTAANNAACAWLEA
QEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGY
FPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREV
LEWRFDSRLAFHHVARELHPEYFKNC

Sequence of entity 2 (D, E), FASTA

>4EMZ_2 MHC-I (chains D, E)
DRKGGSYSQAAGSDSAQGSDVSLTACKV

Sequence of entity 3 (A, M), FASTA

>4EMZ_3 AP-1 complex subunit mu-1 (chains A, M)
SWRSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDK
VLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLI
WIESVIEKHSHSRIEYMVKAKSQFKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPE
NSEIVWSVKSFPGGKEYLMRAHFGLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKI
IEKSGYQALPWVRYITQNGDYQLRTQ

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 Q90VU7), best resolution first:

4EN2 2.58 Å, HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1…
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
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
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…
8D9W 9.3 Å, beta-Arf1 homodimeric interface within AP-1, Arf1, Nef, MHC-I lattice on narrow tubes
8D9V 9.4 Å, gamma-Arf1 homodimeric interface within AP-1, Arf1, Nef lattice on narrow membrane tubes
7UX3 9.6 Å, Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow…
8D4D 9.6 Å, gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I…
8D4F 9.8 Å, beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I…

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