6X5C: Envelope glycoprotein gp160

Asymmetric model of CD4-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52. Determined by electron microscopy at 4.04 Å resolution. Released 21 Oct 2020.

Method: Electron microscopy
Resolution: 4.04 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 9
Atoms: 14,644
Mol. weight: 307.06 kDa
Ligands: UOV, NAG
Released: 21 Oct 2020

Explore 6X5C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X5C contains 74 α-helices and 120 β-strands across 9 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: 10 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	34-40	7	1
β-strand	45-47	3	2
β-strand	53-55	3	3
α-helix	66-68	3
α-helix	70-73	4
β-strand	75	1	3
α-helix	76-77	2
β-strand	84-85	2	2
β-strand	91-94	4	4
α-helix	100-113	14
β-strand	120-124	5	5
β-strand	198-202	5	5
β-strand	215	1	6
β-strand	216-218	3	3
α-helix	219-220	2
β-strand	224-228	5	2
β-strand	236-239	4	4
β-strand	242-245	4	2
β-strand	247	1	3
β-strand	251	1	6
β-strand	257	1	7
β-strand	259-261	3	7
β-strand	271-273	3	7
α-helix	283	1
β-strand	284-298	15	7
β-strand	328-333	6	7
α-helix	335-352	18
β-strand	367	1	8
α-helix	369-372	4
β-strand	374-378	5	7
β-strand	381-385	5	7
β-strand	414-421	8	7
β-strand	423-425	3	5
β-strand	432-434	3	5
α-helix	436-439	4
β-strand	443-455	13	7
β-strand	469-470	2	7
α-helix	475-483	9
β-strand	486-491	6	2
β-strand	494-500	7	1

Chain B: 11 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	518-521	4
α-helix	530-545	16
α-helix	555-559	5
α-helix	562-564	3
α-helix	567-592	26
α-helix	593-596	4
β-strand	603-609	7	1
α-helix	610-611	2
α-helix	619-624	6
α-helix	628-634	7
α-helix	636-638	3
α-helix	639-658	20

Chains C and J: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	8
β-strand	12-17	6	9
β-strand	26-30	5	8
β-strand	35-40	6	8
β-strand	43-46	4	8
β-strand	55-56	2	9
α-helix	59-64	6
β-strand	66-71	6	9
α-helix	76-78	3
β-strand	81-86	6	8
β-strand	92-95	4	8

Chain D: 11 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	10
β-strand	45-47	3	11
β-strand	53-56	4	12
α-helix	66-68	3
α-helix	70-73	4
β-strand	75	1	12
α-helix	76-77	2
β-strand	84-85	2	11
β-strand	91-92	2	13
α-helix	100-113	14
β-strand	120-124	5	14
β-strand	198-202	5	14
β-strand	215-218	4	12
α-helix	219-220	2
β-strand	223-228	6	11
β-strand	238-239	2	13
β-strand	242-245	4	11
β-strand	247	1	12
α-helix	248-250	3
β-strand	251	1	12
β-strand	259-261	3	15
β-strand	271-273	3	15
α-helix	283	1
β-strand	284-298	15	15
β-strand	328-333	6	15
α-helix	335-352	18
β-strand	367	1	16
α-helix	369-372	4
β-strand	374-378	5	15
β-strand	381-386	6	15
β-strand	414-420	7	15
β-strand	423-425	3	14
β-strand	432-434	3	14
α-helix	436-439	4
β-strand	443-444	2	15
β-strand	447-455	9	15
β-strand	469-470	2	15
α-helix	476-482	7
β-strand	486-491	6	11
β-strand	494-499	6	10

Chain E: 12 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	19
β-strand	45-47	3	20
α-helix	51-52	2
β-strand	53-56	4	21
α-helix	65-71	7
β-strand	75	1	21
α-helix	76-78	3
β-strand	84-85	2	22
β-strand	91-94	4	23
α-helix	100-113	14
β-strand	120-123	4	24
β-strand	199-202	4	24
β-strand	215-218	4	21
α-helix	224	1
β-strand	225-228	4	22
β-strand	236-239	4	23
β-strand	242-245	4	22
β-strand	247	1	21
α-helix	248-250	3
β-strand	251	1	21
β-strand	260-261	2	25
β-strand	271-273	3	25
α-helix	283	1
β-strand	284-298	15	25
β-strand	328-333	6	25
α-helix	335-349	15
β-strand	367	1	26
α-helix	369-372	4
β-strand	374-378	5	25
β-strand	381-386	6	25
α-helix	388-390	3
β-strand	414-420	7	25
β-strand	423-425	3	24
β-strand	432-434	3	24
α-helix	436-439	4
β-strand	443-454	12	25
β-strand	455	1	27
β-strand	469	1	27
α-helix	480-483	4
β-strand	486-488	3	22
β-strand	489-491	3	20
β-strand	494-499	6	19

Chain F: 12 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	520-523	4
α-helix	530-545	16
α-helix	555-559	5
α-helix	562-564	3
α-helix	567-592	26
α-helix	593-596	4
β-strand	603-609	7	10
α-helix	610-611	2
α-helix	612-614	3
α-helix	619-625	7
α-helix	628-634	7
α-helix	636-638	3
α-helix	639-658	20

Chain G: 12 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	521-525	5
α-helix	530-545	16
α-helix	551-553	3
α-helix	556-559	4
α-helix	562-564	3
α-helix	568-592	25
α-helix	593-596	4
β-strand	603-609	7	19
α-helix	610-611	2
α-helix	619-624	6
α-helix	628-634	7
α-helix	636-638	3
α-helix	639-657	19

Chain I: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	16
β-strand	14-17	4	17
β-strand	26-30	5	16
β-strand	35-40	6	16
β-strand	43-46	4	16
β-strand	55-56	2	18
α-helix	59-64	6
β-strand	66-69	4	17
β-strand	70-71	2	18
α-helix	76-78	3
β-strand	81-86	6	16
β-strand	92-95	4	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160	A, D, E	protein	524	Human immunodeficiency virus 1	B3UES2
Envelope glycoprotein gp41	B, F, G	protein	153	Human immunodeficiency virus 1	B3UEZ6
T-cell surface glycoprotein CD4	C, I, J	protein	208	Homo sapiens	P01730 (AlphaFold model)

Sequence of entity 1 (A, D, E), FASTA

>6X5C_1 Envelope glycoprotein gp160 (chains A, D, E)
MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCA
SDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQS
LKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMETGEMKNCSFNVTTSIRDKIKK
EYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA
ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTI
IVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQI
VAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTG
GEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR
PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRVVQRRRRRR

Sequence of entity 2 (B, F, G), FASTA

>6X5C_2 Envelope glycoprotein gp41 (chains B, F, G)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD

Sequence of entity 3 (C, I, J), FASTA

>6X5C_3 T-cell surface glycoprotein CD4 (chains C, I, J)
METDTLLLWVLLLWVPGSTGKKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQ
GSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGL
TANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCT
VLQNQKKVEFKIDIVVLAGGSGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
UOV	N-(4'-methyl[1,1'-biphenyl]-4-yl)-1-oxa-7-azaspiro[3.5]nonane-7-carboxamide	C21 H24 N2 O2	3
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	23

Primary citation

A Strain-Specific Inhibitor of Receptor-Bound HIV-1 Targets a Pocket near the Fusion Peptide. Ozorowski, G., Torres, J.L., Santos-Martins, D. et al. Cell Rep (2020) 33:108428-108428. DOI 10.1016/j.celrep.2020.108428 · PubMed

Other PDB entries of the same protein (UniProt B3UES2), best resolution first:

6MUF 2.91 Å, Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in Complex with Human…
6MUG 2.95 Å, Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6OKP 3.28 Å, B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody…
6OPN 3.5 Å, CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35
6OPO 3.5 Å, Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM
6MCO 3.53 Å, Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P23…
5VN8 3.6 Å, Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain…
6X5B 3.6 Å, Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with small molecule…
5VN3 3.7 Å, Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen…
6OPP 3.7 Å, Asymmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM
6OPQ 3.8 Å, CD4- and 17-bound HIV-1 Env B41 SOSIP frozen with LMNG
6MDT 3.82 Å, Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P63…

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