6OPN: CD4- and 17-bound HIV-1 Env B41 SOSIP

CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35. Determined by electron microscopy at 3.5 Å resolution. Released 21 Oct 2020.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 9
Atoms: 14,241
Mol. weight: 308.83 kDa
Ligands: NAG, N07
Released: 21 Oct 2020

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

Secondary structure: helices and β-sheets

6OPN contains 66 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.

Chains A, D and G: 11 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
β-strand	53-56	4	3
α-helix	65-73	9
β-strand	75	1	3
α-helix	76-78	3
β-strand	85	1	2
β-strand	91-92	2	4
α-helix	95-97	3
α-helix	100-115	16
β-strand	120-123	4	5
β-strand	199-202	4	5
β-strand	215-218	4	3
α-helix	219-220	2
β-strand	224-228	5	2
β-strand	238-239	2	4
β-strand	242-245	4	2
β-strand	247	1	3
α-helix	248-250	3
β-strand	251	1	3
β-strand	259-261	3	6
β-strand	271-273	3	6
β-strand	284-298	15	6
β-strand	328-334	7	6
α-helix	335-349	15
β-strand	358-361	3	6
β-strand	367	1	7
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
α-helix	388-390	3
β-strand	413-420	8	6
β-strand	423-425	3	5
β-strand	432-434	3	5
α-helix	436-438	3
β-strand	443-456	14	6
β-strand	466-470	5	6
α-helix	475-483	9
β-strand	486-491	6	2
β-strand	494-499	6	1

Chains B, E and H: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	530-546	17
α-helix	570-592	23
α-helix	593-596	4
β-strand	603-604	2	1
β-strand	609	1	1
α-helix	610	1
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

Chains C, F and I: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	7
β-strand	12-17	6	8
β-strand	26-30	5	7
β-strand	35-40	6	7
β-strand	43-46	4	7
β-strand	55-56	2	8
α-helix	59-64	6
β-strand	66-71	6	8
α-helix	76-78	3
β-strand	81-86	6	7
β-strand	91-94	4	7

Molecules and chains

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

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

>6OPN_1 Envelope glycoprotein gp160 (chains A, D, G)
MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCA
SDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQS
LKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMETGEMKNCSFNVTTSIRDKIKK
EYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA
ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTI
IVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQI
VAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTG
GEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR
PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRVVQRRRRRR

Sequence of entity 2 (B, E, H), FASTA

>6OPN_2 Envelope glycoprotein gp41 (chains B, E, H)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD

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

>6OPN_3 T-cell surface glycoprotein CD4 (chains C, F, I)
METDTLLLWVLLLWVPGSTGKKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQ
GSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGL
TANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCT
VLQNQKKVEFKIDIVVLAGGSGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	27
N07	[3'-(5-methyl-1,3,4-oxadiazol-2-yl)[1,1'-biphenyl]-3-yl](piperidin-1-yl)methano…	C21 H21 N3 O2	3

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…
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…
6U59 3.86 Å, HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B

Browse structure collections

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