6OKP: B41 SOSIP.664

B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody 10-1074. Determined by electron microscopy at 3.28 Å resolution. Released 5 Jun 2019.

Method: Electron microscopy
Resolution: 3.28 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 14
Atoms: 22,857
Mol. weight: 453.21 kDa
Ligands: NAG
Released: 5 Jun 2019

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

Secondary structure: helices and β-sheets

6OKP contains 61 α-helices and 242 β-strands across 14 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, B and C: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	572-594	23
β-strand	603-609	7	1
α-helix	610-611	2
α-helix	619-622	4
α-helix	629-634	6
α-helix	636-638	3
α-helix	639-647	9
α-helix	648-652	5
α-helix	653-662	10

Chain D: 7 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	4
β-strand	53-54	2	5
α-helix	74-78	5
β-strand	84-85	2	4
β-strand	92	1	6
α-helix	100-109	10
β-strand	121	1	7
α-helix	123-125	3
β-strand	129-133	5	8
β-strand	154-161	8	8
β-strand	170-177	8	8
β-strand	181-183	3	8
β-strand	190-193	4	8
β-strand	200	1	9
β-strand	202	1	7
β-strand	203	1	10
α-helix	204-205	2
β-strand	215	1	11
β-strand	217-218	2	5
β-strand	223-228	6	4
β-strand	238	1	6
β-strand	242-245	4	4
β-strand	247	1	5
β-strand	251	1	11
β-strand	259	1	12
β-strand	271-273	3	12
β-strand	284-287	4	12
β-strand	292-293	2	13
β-strand	297-304	8	8
β-strand	307-308	2	14
β-strand	316-317	2	14
β-strand	320-322	4	8
β-strand	330	1	8
β-strand	333	1	15
α-helix	336-352	17
β-strand	357-361	4	16
β-strand	374-379	6	17
β-strand	381-385	5	17
β-strand	394-395	2	16
β-strand	414	1	15
β-strand	417	1	8
β-strand	420	1	17
β-strand	423	1	10
β-strand	432	1	9
β-strand	435	1	10
α-helix	437-440	4
β-strand	441-444	4	8
β-strand	448-449	2	13
β-strand	452-454	3	12
β-strand	455	1	18
β-strand	465-468	4	16
β-strand	469	1	18
α-helix	476-478	3
β-strand	486-491	6	4
β-strand	494-499	6	1

Chain E: 8 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	2
β-strand	45-47	3	19
β-strand	53-55	3	20
β-strand	75	1	20
α-helix	76-78	3
β-strand	84-85	2	19
β-strand	92-93	2	21
α-helix	99-114	16
β-strand	120-121	2	22
α-helix	123-125	3
β-strand	129-130	2	23
β-strand	133	1	23
β-strand	154-162	9	23
β-strand	169-177	9	23
β-strand	181-183	3	23
β-strand	190-193	4	23
β-strand	200	1	24
β-strand	202-203	2	22
α-helix	204-205	2
β-strand	215	1	25
β-strand	216-218	3	20
β-strand	223-228	6	19
β-strand	237-238	2	21
β-strand	242-245	4	19
β-strand	247	1	20
β-strand	251	1	25
β-strand	259-260	2	26
β-strand	271-273	3	26
β-strand	284-293	10	26
β-strand	297-302	6	27
β-strand	307-308	2	28
β-strand	316-317	2	28
β-strand	320	1	23
β-strand	322-323	2	27
β-strand	333	1	29
α-helix	335-352	18
β-strand	357-361	4	30
α-helix	369-372	4
β-strand	374-379	6	31
β-strand	381-385	5	31
β-strand	394-395	2	30
β-strand	414	1	29
β-strand	420	1	31
β-strand	423	1	22
β-strand	432	1	24
β-strand	435	1	22
α-helix	436-439	4
β-strand	441-444	4	27
β-strand	448-454	7	26
β-strand	455	1	32
β-strand	465-468	4	30
β-strand	469	1	32
α-helix	476-478	3
β-strand	486-491	6	19
β-strand	494-499	6	2

Chain F: 8 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	3
β-strand	45-47	3	33
β-strand	53-55	3	34
α-helix	75-78	4
β-strand	84-85	2	33
β-strand	92	1	35
α-helix	99-111	13
β-strand	120-121	2	36
α-helix	123-125	3
β-strand	129-133	5	37
β-strand	154-162	9	37
β-strand	169-177	9	37
β-strand	181-183	3	37
β-strand	190-193	4	37
β-strand	200	1	38
β-strand	202-203	2	36
α-helix	204-205	2
β-strand	215	1	39
β-strand	216-218	3	34
β-strand	223-228	6	33
β-strand	238	1	35
β-strand	242-245	4	33
β-strand	247	1	34
β-strand	251	1	39
β-strand	259	1	40
β-strand	271-274	4	40
β-strand	284-287	4	40
β-strand	292-294	3	41
β-strand	297-298	2	42
β-strand	302-304	3	37
β-strand	307-308	2	43
β-strand	316-317	2	43
β-strand	320-322	4	37
β-strand	333	1	41
α-helix	336-352	17
β-strand	357-361	4	44
β-strand	374-379	6	45
β-strand	381-385	5	45
β-strand	394-395	2	44
β-strand	414	1	41
β-strand	420	1	45
β-strand	423	1	36
α-helix	426-428	3
β-strand	432	1	38
β-strand	435	1	36
α-helix	436-440	5
β-strand	443-444	2	42
β-strand	447-449	3	41
β-strand	452-454	3	40
β-strand	455-456	2	44
β-strand	465-469	5	44
α-helix	477-480	4
β-strand	486-491	6	33
β-strand	494-499	6	3

Chain K: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	46
β-strand	11-12	2	47
β-strand	18	1	48
β-strand	21-25	5	46
α-helix	29-31	3
β-strand	33-39	7	49
β-strand	45-47	3	49
β-strand	51	1	49
β-strand	67-68	2	48
β-strand	71-72	2	46
β-strand	77-78	2	46
β-strand	81-82	2	48
α-helix	84-86	3
β-strand	88-95	8	49
β-strand	96-100A	6	50
α-helix	100E-100G	3
β-strand	100J-100O	6	50
β-strand	103	1	49
β-strand	107-109	3	49
β-strand	110-111	2	47

Chain L: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-14	2
β-strand	18-22	5	51
β-strand	31	1	52
β-strand	36-38	3	53
β-strand	44-46	3	53
β-strand	49	1	54
β-strand	53	1	54
β-strand	62-63	2	51
β-strand	72-76	5	51
α-helix	80-82	3
β-strand	85-87	3	53
β-strand	92	1	52
β-strand	97	1	49

Chains M, O and Q: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	55
β-strand	11-12	2	56
β-strand	17-24	8	55
β-strand	33-39	7	57
β-strand	46-52	7	57
β-strand	57-59	3	57
α-helix	64-66	3
β-strand	67-72	6	55
β-strand	77-82A	7	55
α-helix	84-86	3
β-strand	88-94	7	57
β-strand	101	1	57
β-strand	107-109	3	57
β-strand	110-111	2	56

Chains N, P and R: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	58
β-strand	10-13	4	59
β-strand	19-20	2	58
β-strand	22-25	4	58
β-strand	34-38	5	59
β-strand	45-49	5	59
β-strand	53-54	2	59
α-helix	55	1
β-strand	62-67	6	58
β-strand	70-75	6	58
β-strand	85-89	5	59
β-strand	99-103	5	59

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp41	A, B, C	protein	153	Human immunodeficiency virus 1	B3UEZ6
Envelope glycoprotein gp120	D, E, F	protein	516	Human immunodeficiency virus 1	B3UES2
10-1074 Heavy Chain,10-1074 Heavy Chain	K	protein	244	Homo sapiens	S6B291 (AlphaFold model)
10-1074 Light Chain,10-1074 Light Chain	L	protein	214	Homo sapiens	Q8N5F4 (AlphaFold model)
SF12 Heavy Chain,SF12 Heavy Chain	M, O, Q	protein	241	Homo sapiens	S6B291 (AlphaFold model)
SF12 Light Chain,SF12 Light Chain	N, P, R	protein	212	Homo sapiens	P01834

Sequence of entity 1 (A, B, C), FASTA

>6OKP_1 Envelope glycoprotein gp41 (chains A, B, C)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD

Sequence of entity 2 (D, E, F), FASTA

>6OKP_2 Envelope glycoprotein gp120 (chains D, E, F)
MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCA
SDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQS
LKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMETGEMKNCSFNVTTSIRDKIKK
EYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA
ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTI
IVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQI
VAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCNTTPLFNSTWNNTRTDDYPTG
GEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR
PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV

Sequence of entity 3 (K), FASTA

>6OKP_3 10-1074 Heavy Chain,10-1074 Heavy Chain (chains K)
QVQLQESGPGLVKPSETLSVTCSVSGDSMNNYYWTWIRQSPGKGLEWIGYISDRESATYN
PSLNSRVVISRDTSKNQLSLKLNSVTPADTAVYYCATARRGQRIYGVVSFGEFFYYYSMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHH
HHHH

Sequence of entity 4 (L), FASTA

>6OKP_4 10-1074 Light Chain,10-1074 Light Chain (chains L)
SYVRPLSVALGETARISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERFSGT
PDINFGTRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 5 (M, O, Q), FASTA

>6OKP_5 SF12 Heavy Chain,SF12 Heavy Chain (chains M, O, Q)
QVQLQESGPGLVKPSETLSVTCRVSGGSLDLYYWSWIRQPPGKGLQWIGFVYFDGSYGDY
DPSLRSRVTISADMSKNQISLRLKSVTPADTAVYYCARLGPGGIFDRWTGHYGDKWLDPW
GQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHH
H

Sequence of entity 6 (N, P, R), FASTA

>6OKP_6 SF12 Light Chain,SF12 Light Chain (chains N, P, R)
QIDLTQSPRTLSLSAGERATLLCRASQSVSNVALAWYQHKPGQAPRLLLHEASTRATGIP
DRFIGSGSGRDFTLTITSLEPEDFAVYYCQLSGRRLGQGTKVEIKRTVAAPSVFIFPPSD
EQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLS
KADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	33

Primary citation

Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope. Schoofs, T., Barnes, C.O., Suh-Toma, N. et al. Immunity (2019) 50:1513. DOI 10.1016/j.immuni.2019.04.014 · 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…
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…
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
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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