9Q0W: HIV-1 BG505DS-SOSIP.664 Env Trimer

Cryo-EM Structure of HIV-1 BG505DS-SOSIP.664 Env Trimer Bound to DFPH-a.01_10R59P_LC Fab. Determined by electron microscopy at 3.0 Å resolution. Released 10 Dec 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Human immunodeficiency virus 1, Macaca
Chains: 12
Atoms: 24,735
Mol. weight: 376.3 kDa
Ligands: NAG
Released: 10 Dec 2025

Explore 9Q0W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q0W contains 101 α-helices and 284 β-strands across 12 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: 11 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
β-strand	53-55	3	3
β-strand	56	1	4
β-strand	67	1	5
α-helix	75	1
β-strand	76	1	4
α-helix	77-78	2
β-strand	83-86	4	2
β-strand	91-94	4	6
α-helix	99-116	18
β-strand	121-122	2	7
β-strand	129-133	5	8
β-strand	138	1	9
β-strand	154-162	9	8
β-strand	169-177	9	8
β-strand	181-183	3	8
β-strand	190-193	4	8
α-helix	194-197	4
β-strand	201-203	3	7
α-helix	204-205	2
β-strand	209	1	5
β-strand	215	1	10
β-strand	216-218	3	3
β-strand	223-228	6	2
β-strand	236-239	4	6
β-strand	242-245	4	2
β-strand	251	1	10
β-strand	260-261	2	11
β-strand	271-273	3	11
α-helix	283	1
β-strand	284-302	19	11
β-strand	304-312	7	12
β-strand	315-320	6	12
β-strand	326	1	9
β-strand	330-334	5	11
α-helix	335-350	16
β-strand	358-361	4	11
α-helix	369-372	4
β-strand	374-378	5	13
β-strand	381-385	5	13
β-strand	393-395	3	11
β-strand	413-417	5	11
β-strand	418-421	4	13
β-strand	423-424	2	7
β-strand	433-435	3	7
α-helix	437-439	3
β-strand	441-457	17	11
β-strand	465-470	6	11
α-helix	476-480	5
α-helix	483-485	3
β-strand	486-491	6	2
β-strand	494-499	6	1

Chain B: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	517	1	14
β-strand	518-519	2	15
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-542	6
α-helix	570-594	25
β-strand	603-609	7	1
α-helix	612-614	3
α-helix	619-623	5
α-helix	628-634	7
α-helix	639-662	24

Chain C: 12 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	16
β-strand	45-47	3	17
β-strand	53-56	4	18
β-strand	67	1	19
β-strand	75-76	2	18
α-helix	77-78	2
β-strand	83-85	3	17
β-strand	91-94	4	20
α-helix	95-97	3
α-helix	99-115	17
β-strand	121	1	21
β-strand	129-133	5	22
β-strand	138	1	23
α-helix	140-150	3
β-strand	154-162	9	22
β-strand	169-177	9	22
α-helix	178-180	3
β-strand	181-183	3	22
β-strand	190-193	4	22
β-strand	201-203	3	21
α-helix	204-205	2
β-strand	209	1	19
β-strand	215	1	24
β-strand	216-218	3	18
β-strand	223-228	6	17
β-strand	236-239	4	20
β-strand	242-245	4	17
β-strand	247	1	18
β-strand	251	1	24
β-strand	256	1	25
β-strand	260-261	2	25
α-helix	264-266	3
β-strand	271-273	3	25
β-strand	284-298	15	25
β-strand	301-312	10	26
β-strand	315-323	10	26
β-strand	326	1	23
β-strand	329-334	6	25
α-helix	335-349	15
α-helix	350-352	3
β-strand	358-361	4	25
α-helix	369-372	4
β-strand	374-378	5	25
β-strand	381-385	5	25
β-strand	393-395	3	25
β-strand	413-420	8	25
β-strand	423-424	2	21
β-strand	433-435	3	21
α-helix	436-440	5
β-strand	443-456	14	25
β-strand	465-470	6	25
α-helix	476-483	8
β-strand	486-491	6	17
β-strand	495-499	5	16

Chain D: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	516-519	4	27
α-helix	520-521	2
β-strand	529	1	28
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-541	5
α-helix	570-595	26
β-strand	603-609	7	16
α-helix	619-625	7
β-strand	627	1	28
α-helix	628-634	7
α-helix	639-661	23

Chain E: 12 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	29
β-strand	45-47	3	30
α-helix	52	1
β-strand	53-56	4	31
β-strand	67	1	32
β-strand	75-76	2	31
α-helix	77-78	2
β-strand	83-86	4	30
β-strand	91-94	4	33
α-helix	95-97	3
α-helix	99-116	18
β-strand	121	1	34
β-strand	129-133	5	35
β-strand	138	1	36
α-helix	140-150	3
β-strand	154-162	9	35
β-strand	169-177	9	35
β-strand	181-183	3	35
β-strand	190-193	4	35
α-helix	194-197	4
β-strand	201-203	3	34
α-helix	204-205	2
β-strand	209	1	32
β-strand	215	1	37
β-strand	216-218	3	31
β-strand	223-228	6	30
β-strand	236-239	4	33
β-strand	242-245	4	30
β-strand	247	1	31
β-strand	251	1	37
β-strand	260-261	2	38
α-helix	264-266	3
β-strand	271-274	4	38
β-strand	284-298	15	38
β-strand	302-312	9	39
β-strand	315-322	9	39
β-strand	326	1	36
β-strand	329-334	6	38
α-helix	335-353	19
β-strand	358-361	4	38
α-helix	369-372	4
β-strand	374-378	5	38
β-strand	381-385	5	38
β-strand	393-395	3	38
β-strand	413-421	9	38
β-strand	423-424	2	34
β-strand	433-435	3	34
α-helix	436-439	4
β-strand	443-457	15	38
β-strand	465-470	6	38
α-helix	476-483	8
β-strand	486-491	6	30
β-strand	494-499	6	29

Chain F: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	517-519	3	40
α-helix	530-533	4
α-helix	537-542	6
α-helix	572-595	24
β-strand	603-609	7	29
α-helix	628-634	7
α-helix	639-662	24

Chain G: 7 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	41
β-strand	11-13	3	42
β-strand	18-25	8	41
β-strand	33	1	14
β-strand	35-39	7	43
β-strand	45-52	8	43
β-strand	57-59	3	43
β-strand	67-72	6	41
β-strand	77-82	6	41
α-helix	84-86	3
β-strand	88-95	8	43
β-strand	97-100A	5	15
β-strand	100D-100I	6	15
β-strand	102-103	2	43
β-strand	107-109	3	43
β-strand	110-112	3	42
β-strand	117	1	44
α-helix	118-119	2
β-strand	120-124	5	45
α-helix	125-127	3
α-helix	128-131	4
β-strand	135-145	11	45
β-strand	146	1	44
β-strand	151-154	4	46
α-helix	155-157	3
β-strand	159	1	46
β-strand	163-165	3	45
α-helix	166-168	3
β-strand	169-170	2	45
β-strand	176-185	10	45
α-helix	186-188	3
β-strand	189	1	47
β-strand	192	1	47
β-strand	194-200	7	46
β-strand	205-211	7	46

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	48
β-strand	10-13	4	49
β-strand	19-25	7	48
β-strand	29	1	50
β-strand	31	1	50
β-strand	33-38	6	51
β-strand	45-49	5	51
β-strand	53-54	2	51
α-helix	55	1
β-strand	62-67	6	48
β-strand	70-75	6	48
α-helix	80-82	3
β-strand	85-90	6	51
β-strand	102	1	51
β-strand	103-106	4	49
β-strand	111	1	52
α-helix	112-113	2
β-strand	114-118	5	53
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	53
β-strand	140	1	52
β-strand	144-150	7	54
β-strand	153-155	3	54
β-strand	159-163	5	53
α-helix	164-167	4
β-strand	173-182	10	53
α-helix	183-187	5
β-strand	191-198	8	54
β-strand	205-210	6	54

4 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
HIV-1 BG505 ds-sosip gp120	A, C, E	protein	481	Human immunodeficiency virus 1	Q2N0S6
BG505 ds-sosip GP41	B, D, F	protein	153	Human immunodeficiency virus 1	Q2N0S5
DFPH-a.01_10R59P_LC Fab heavy chain	G, I, K	protein	233	Macaca
DFPH-a.01_10R59P_LC Fab light chain	H, J, L	protein	214	Macaca

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

>9Q0W_1 HIV-1 BG505 DS-SOSIP gp120 (chains A, C, E)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

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

>9Q0W_2 BG505 DS-SOSIP GP41 (chains B, D, F)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 3 (G, I, K), FASTA

>9Q0W_3 DFPH-a.01_10R59P_LC Fab heavy chain (chains G, I, K)
QVQLQVSGPGVVKASETLSLTCDVSSASNTRDYFYWSWVRQSPGKGLEWIGGVYSNSDTS
NKNPSLESRVTISKDTSKNRFFLRLNSVTAADTAVYYCSSRAKIYFAVGYDSGGRIDVWG
PGVLVTVATASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVH
TFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCG

Sequence of entity 4 (H, J, L), FASTA

>9Q0W_4 DFPH-a.01_10R59P_LC Fab light chain (chains H, J, L)
DIQMTQSPSRLSASVGDRVTVTCRASQDIDKDLSWFQQKPGKAPTLLIFTASSLQTGVPS
RFSGSGSGTEFTLTISSLQPEDFATYFCQQDYSFPLTFGGGTKVDLKRTVAAPSVFIFPP
SEDQVKSGTVSVVCLLNNFYPREASVKWKVDGALKTGNSQESVTEQDSKDNTYSLSSTLT
LSSTEYQSHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	18

Primary citation

Yeast Display Reveals Plentiful Mutations That Improve Fusion Peptide Vaccine-Elicited Antibodies Beyond 59% HIV-1 Neutralization Breadth. Franca, C.T., Pletnev, S., Madan, B. et al. Vaccines (Basel) (2025) 13. DOI 10.3390/vaccines13111098 · PubMed

Other PDB entries of the same protein (UniProt Q2N0S6), best resolution first:

8TOX 2.3 Å, Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab
6MTJ 2.34 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6W03 2.4 Å, Crystal Structure of HIV-1 BG505 DS-SOSIP.3mut Prefusion Env Trimer in Complex with…
6MTN 2.5 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6UDJ 2.5 Å, HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074
8FR6 2.5 Å, Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6MU7 2.5 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6MU6 2.55 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6NNJ 2.6 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to CH31 scFv in…
8EUV 2.6 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-COMBO1 FAB
8T4K 2.6 Å, MD64 N332-GT5 sosip
8EUU 2.7 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01 FAB

Browse structure collections

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