6OPP: 17b Fab light chain

Asymmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM. Determined by electron microscopy at 3.7 Å resolution. Released 21 Oct 2020.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 15
Atoms: 21,852
Mol. weight: 467.58 kDa
Ligands: NAG, LMT
Released: 21 Oct 2020

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

Secondary structure: helices and β-sheets

6OPP contains 79 α-helices and 201 β-strands across 15 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: 12 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	4
β-strand	45-47	3	5
α-helix	51-52	2
β-strand	53-55	3	6
α-helix	65-73	9
β-strand	75	1	6
α-helix	76-78	3
β-strand	83-85	3	5
β-strand	91-94	4	7
α-helix	95-97	3
α-helix	100-115	16
β-strand	120-126	7	8
β-strand	196-202	7	8
β-strand	215	1	9
β-strand	216-218	3	6
α-helix	219-220	2
β-strand	223-228	6	5
β-strand	236-239	4	7
β-strand	242-245	4	5
β-strand	247	1	6
α-helix	248-250	3
β-strand	251	1	9
β-strand	259-261	3	10
β-strand	271-273	3	10
α-helix	283	1
β-strand	284-298	15	10
β-strand	328-334	7	10
α-helix	335-349	15
β-strand	357-361	4	10
β-strand	367	1	11
α-helix	369-372	4
β-strand	374-378	5	10
β-strand	381-385	5	10
β-strand	394-395	2	10
β-strand	400	1	10
β-strand	413-421	9	10
β-strand	423-425	3	8
β-strand	432-434	3	8
α-helix	436-439	4
β-strand	443-457	15	10
β-strand	465-470	6	10
α-helix	475-483	9
β-strand	486-491	6	5
β-strand	494-499	6	4

Chain B: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	529	1	3
α-helix	530-545	16
α-helix	568-592	25
α-helix	593-596	4
β-strand	603-609	7	4
α-helix	610-611	2
α-helix	619-625	7
β-strand	627	1	3
α-helix	628-634	7
α-helix	636-638	3
α-helix	639-663	25

Chain C: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	11
β-strand	12-17	6	12
β-strand	26-29	4	11
β-strand	35-40	6	11
β-strand	43-46	4	11
β-strand	55-56	2	12
α-helix	59-64	6
β-strand	66-71	6	12
α-helix	76-78	3
β-strand	81-86	6	11
β-strand	89	1	11
β-strand	92-96	5	11

Chain D: 10 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	17
β-strand	45-47	3	18
α-helix	51-52	2
β-strand	53-55	3	19
α-helix	65-73	9
β-strand	75	1	19
α-helix	76-77	2
β-strand	83-85	3	18
β-strand	91-94	4	20
α-helix	99-113	15
β-strand	120-123	4	21
β-strand	126	1	22
β-strand	196	1	22
β-strand	199-202	4	21
β-strand	215	1	23
β-strand	216-218	3	19
α-helix	219-220	2
β-strand	223-228	6	18
β-strand	236-239	4	20
β-strand	242-245	4	18
β-strand	247	1	19
α-helix	248-250	3
β-strand	251	1	23
β-strand	259-260	2	24
β-strand	271-274	4	24
β-strand	283-298	16	24
β-strand	328-334	7	24
α-helix	335-349	15
β-strand	357-361	4	24
β-strand	367	1	25
α-helix	369-372	4
β-strand	374-378	5	24
β-strand	381-385	5	24
β-strand	394-395	2	24
β-strand	400	1	24
β-strand	413-421	9	24
β-strand	423-425	3	21
β-strand	432-434	3	21
α-helix	436-439	4
β-strand	443-457	15	24
β-strand	465-470	6	24
α-helix	475-483	9
β-strand	486-491	6	18
β-strand	494-499	6	17

Chain E: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	529	1	26
α-helix	530-546	17
α-helix	568-592	25
α-helix	593-596	4
β-strand	603-609	7	17
α-helix	610-611	2
α-helix	619-625	7
β-strand	627	1	26
α-helix	628-634	7
α-helix	636-638	3
α-helix	639-660	22

Chain F: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	25
β-strand	12-17	6	45
β-strand	26-29	4	25
β-strand	35-40	6	25
β-strand	43-46	4	25
β-strand	55-56	2	45
α-helix	59-64	6
β-strand	66-71	6	45
α-helix	76-78	3
β-strand	81-86	6	25
β-strand	89-96	8	25

Chain G: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	27
β-strand	10-12	3	28
β-strand	18-25	8	27
α-helix	29-31	3
β-strand	33-39	7	28
β-strand	45-52	8	28
β-strand	56-59	4	28
β-strand	67-72	6	27
α-helix	73-75	3
β-strand	77-82	6	27
α-helix	84-86	3
β-strand	88-95	8	28
α-helix	100-100B	3
β-strand	102-103	2	28
β-strand	107-111	5	28

Chain H: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	13
β-strand	10-12	3	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	34-39	6	14
β-strand	45-52	8	14
β-strand	56-59	4	14
β-strand	67-72	6	13
β-strand	77-82	6	13
α-helix	84-86	3
β-strand	88-94	7	14
α-helix	100-100B	3
β-strand	102-103	2	14
β-strand	107-111	5	14

7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
17b Fab light chain	I, L, O	protein	214	Homo sapiens
Envelope glycoprotein gp41	B, E, K	protein	153	Human immunodeficiency virus 1	B3UEZ6
Envelope glycoprotein gp160	A, D, J	protein	524	Human immunodeficiency virus 1	B3UES2
T-cell surface glycoprotein CD4	C, F, M	protein	208	Homo sapiens	P01730 (AlphaFold model)
17b Fab heavy chain	G, H, N	protein	229	Homo sapiens

Sequence of entity 1 (I, L, O), FASTA

>6OPP_1 17b Fab light chain (chains I, L, O)
ELELTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPA
RFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

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

>6OPP_2 Envelope glycoprotein gp41 (chains B, E, K)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD

Sequence of entity 3 (A, D, J), FASTA

>6OPP_3 Envelope glycoprotein gp160 (chains A, D, J)
MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCA
SDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQS
LKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMETGEMKNCSFNVTTSIRDKIKK
EYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA
ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTI
IVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQI
VAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTG
GEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR
PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRVVQRRRRRR

Sequence of entity 4 (C, F, M), FASTA

>6OPP_4 T-cell surface glycoprotein CD4 (chains C, F, M)
METDTLLLWVLLLWVPGSTGKKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQ
GSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGL
TANSDTHLLQGQSLTLTLESPPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCT
VLQNQKKVEFKIDIVVLAGGSGHHHHHH

Sequence of entity 5 (G, H, N), FASTA

>6OPP_5 17b Fab heavy chain (chains G, H, N)
QVQLLESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHY
APHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQ
GTLVTVTSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	24
LMT	Dodecyl-beta-D-maltoside	C24 H46 O11	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 B3UEZ6), 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
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…
6OPQ 3.8 Å, CD4- and 17-bound HIV-1 Env B41 SOSIP frozen with LMNG
6U59 3.86 Å, HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B
6X5C 4.04 Å, Asymmetric model of CD4-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52
6EDU 4.06 Å, B41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-receptor mimicking antibody…

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