9Q3S: PGT121 Fab and Rhesus macaque Ab4 Fab

Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664. Determined by electron microscopy at 3.01 Å resolution. Released 27 May 2026.

Method: Electron microscopy
Resolution: 3.01 Å
Organisms: Human immunodeficiency virus 1, Macaca mulatta, Homo sapiens
Chains: 18
Atoms: 26,619
Mol. weight: 528.34 kDa
Ligands: NAG
Released: 27 May 2026

Explore 9Q3S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Q3S contains 76 α-helices and 280 β-strands across 18 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: 13 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	23
β-strand	45-47	3	24
α-helix	51-52	2
β-strand	53-56	4	25
α-helix	58-61	4
α-helix	71-73	3
β-strand	75-76	2	25
α-helix	77	1
β-strand	83-86	4	24
β-strand	91-94	4	26
α-helix	102-114	13
α-helix	120	1
β-strand	121	1	27
β-strand	129-131	3	28
β-strand	132-133	2	29
β-strand	154-162	9	29
β-strand	169-177	9	29
β-strand	181-183	3	28
β-strand	189-193	5	28
α-helix	194-197	4
β-strand	200-203	4	27
α-helix	204-205	2
β-strand	215	1	30
β-strand	216-218	3	25
β-strand	223-228	6	24
β-strand	236-239	4	26
β-strand	242-245	4	24
β-strand	247	1	25
β-strand	251	1	30
β-strand	261	1	31
β-strand	271-273	3	31
β-strand	284-312	27	31
β-strand	315-322	9	31
β-strand	330-334	5	31
α-helix	335-353	19
β-strand	358-361	4	31
α-helix	369-372	4
β-strand	374-378	5	32
β-strand	381-385	5	32
β-strand	393-395	3	31
β-strand	413-417	5	31
β-strand	420-421	2	32
β-strand	423-424	2	27
β-strand	432-435	4	27
α-helix	436-440	5
β-strand	441-456	16	31
α-helix	457	1
α-helix	460-462	3
β-strand	465-470	6	31
β-strand	488-491	4	24
β-strand	494-499	6	23

Chain B: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	537-541	5
α-helix	570-573	4
α-helix	577-595	19
β-strand	604-609	6	1
α-helix	620-623	4
α-helix	628-635	8
α-helix	636-638	3
α-helix	642-658	17

Chains C and J: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	537-541	5
α-helix	570-573	4
α-helix	577-595	19
β-strand	604-609	6	23
α-helix	620-623	4
α-helix	628-635	8
α-helix	642-658	17

Chain d: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	41
β-strand	11-12	2	42
β-strand	22	1	41
β-strand	33-40	8	43
β-strand	43-51	9	43
β-strand	58-59	2	43
β-strand	70-72	3	44
β-strand	77-79	3	44
β-strand	88-96	9	43
β-strand	100-100A	2	45
α-helix	100E-100G	3
β-strand	100J-100K	2	45
β-strand	100O-101	5	43
β-strand	105-107	3	43
β-strand	108-109	2	42

Chain D: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	33
β-strand	18-25	8	33
β-strand	36-38	3	34
β-strand	46-51	6	34
β-strand	57-59	3	34
β-strand	67-72	6	33
β-strand	77-82	6	33
α-helix	84-86	3
β-strand	88-90	3	35
β-strand	93	1	36
β-strand	103	1	36
β-strand	107-109	3	35

Chain e: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	46
β-strand	18-22	5	47
β-strand	31	1	48
β-strand	34-38	5	46
β-strand	45-48	4	46
β-strand	62-63	2	47
β-strand	72-76	5	47
β-strand	85-89	5	46
β-strand	92	1	48
β-strand	95	1	48
α-helix	95A-95C	3
β-strand	97	1	43
β-strand	99	1	46
β-strand	103-106	4	46

Chain E: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	37
β-strand	9-13	4	38
β-strand	19-20	2	39
β-strand	23-24	2	37
α-helix	29-31	3
β-strand	34-38	5	38
β-strand	44-49	6	38
β-strand	53-54	2	38
β-strand	62	1	39
β-strand	65	1	40
β-strand	71	1	37
β-strand	72	1	40
β-strand	74-75	2	39
α-helix	80-82	3
β-strand	84-86	3	38
β-strand	88-90	3	38
α-helix	96	1
β-strand	97-98	2	38
α-helix	99	1
β-strand	102-106	5	38

Chain G: 14 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
α-helix	51-52	2
β-strand	53-56	4	3
α-helix	58-61	4
α-helix	71-73	3
β-strand	75-76	2	3
α-helix	77	1
β-strand	83-86	4	2
β-strand	91-94	4	4
α-helix	102-114	13
α-helix	120	1
β-strand	121	1	5
β-strand	129-131	3	6
β-strand	132-133	2	7
β-strand	154-162	9	7
β-strand	169-177	9	7
β-strand	181-183	3	6
β-strand	189-193	5	6
α-helix	194-197	4
β-strand	200-203	4	5
α-helix	204-205	2
β-strand	215	1	8
β-strand	216-218	3	3
β-strand	223-228	6	2
β-strand	236-239	4	4
β-strand	242-245	4	2
β-strand	247	1	3
β-strand	251	1	8
β-strand	256	1	9
β-strand	261	1	10
β-strand	271-273	3	10
β-strand	284-312	27	10
β-strand	315-322	9	10
β-strand	330-334	5	10
α-helix	335-353	19
β-strand	358-361	4	10
α-helix	369-372	4
β-strand	374-378	5	9
β-strand	381-385	5	9
α-helix	387-389	3
β-strand	393-395	3	10
β-strand	413-417	5	10
β-strand	420-421	2	9
β-strand	423-424	2	5
β-strand	432-435	4	5
α-helix	437-439	3
β-strand	441-456	16	10
α-helix	457	1
α-helix	460-462	3
β-strand	465-470	6	10
β-strand	488-491	4	2
β-strand	494-499	6	1

9 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
BG505 SOSIP.664 gp41	B, C, J	protein	153	Human immunodeficiency virus 1	Q2N0S5
BG505 SOSIP.664 gp120	A, G, I	protein	481	Human immunodeficiency virus 1	Q2N0S5
Ab 4 Fab heavy chain	D, H, K	protein	229	Macaca mulatta
Ab 4 Fab light chain	E, L, M	protein	215	Macaca mulatta
PGT121 Fab heavy chain	d, h, k	protein	235	Homo sapiens
PGT121 Fab light chain	e, l, m	protein	213	Homo sapiens

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

>9Q3S_1 BG505 SOSIP.664 gp41 (chains B, C, J)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 2 (A, G, I), FASTA

>9Q3S_2 BG505 SOSIP.664 gp120 (chains A, G, I)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

Sequence of entity 3 (D, H, K), FASTA

>9Q3S_3 Ab 4 Fab heavy chain (chains D, H, K)
QLQLQESGPGLVKPSETLSVTCDVSGGSISDNFWIWIRQAPGQGLEWIGYMYGTNGGTNV
NPSFKGRVTLSADTSKNQLSLKVDSVTVADTAVYYCVRYWNRWGTGYFDYWGQGVLVTVS
SASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGGSK

Sequence of entity 4 (E, L, M), FASTA

>9Q3S_4 Ab 4 Fab light chain (chains E, L, M)
QAVVTQEPSMTVSPGGTVTLTCASSTGAVAIGHTPHWFQQKPGQVPRALIYHSDQKHSGT
PARFSGSLLGDKAALTLSGALPEDEAEYYCWLAFSSGGVFGSGTKLTVLGQPKASPLVTL
FPPSSEELQANKATLVCLISDFYPGVVKVAWKADGNSVNTGVETTTPSKQSNNKYAASSY
LSLTSDQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 5 (d, h, k), FASTA

>9Q3S_5 PGT121 Fab heavy chain (chains d, h, k)
QMQLQESGPGLVKPSETLSLTCSVSGASISDSYWSWIRRSPGKGLEWIGYVHKSGDTNYS
PSLKSRVNLSLDTSKNQVSLSLVAATAADSGKYYCARTLHGRRIYGIVAFNEWFTYFYMD
VWGNGTQVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 6 (e, l, m), FASTA

>9Q3S_6 PGT121 Fab light chain (chains e, l, m)
QVQIDISVAPGETARISCGEKSLGSRAVQWYQHRAGQAPSLIIYNNQDRPSGIPERFSGS
PDSPFGTTATLTITSVEAGDEADYYCHIWDSRVPTKWVFGGGTTLTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	21

Primary citation

Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 Fab in complex with HIV-1 Env trimer BG505 SOSIP.664. Chandravanshi, M., Tolbert, W.D., Pazgier, M. To be published.

Other PDB entries of the same protein (UniProt Q2N0S5), best resolution first:

6CDO 2.1 Å, Structure of vaccine-elicited HIV-1 neutralizing antibody vFP16.02 in complex with HIV-1…
6CDM 2.41 Å, Structure of vaccine-elicited HIV-1 neutralizing antibody vFP7.04 in complex with HIV-1…
6CDP 2.46 Å, Vaccine-elicited HIV-1 neutralizing antibody vFP20.01 in complex with HIV-1 fusion…
9P6E 2.7 Å, N49P7-FR Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab
9P6G 2.7 Å, eN49P7-FRv1-23 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab
8TTW 2.96 Å, Cryo-EM structure of BG505 SOSIP.664 HIV-1 Env trimer in complex with temsavir, 8ANC195,…
9Y9V 2.98 Å, The cryoem structure of rhesus macaque 1A8 and PGT121 fabs in complex with BG505…
9Q0W 3.0 Å, Cryo-EM Structure of HIV-1 BG505DS-SOSIP.664 Env Trimer Bound to DFPH-a.01_10R59P_LC Fab
5U7M 3.02 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
5U7O 3.03 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
4TVP 3.1 Å, Crystal Structure of the HIV-1 BG505 SOSIP.664 Env Trimer Ectodomain, Comprising…
8TKC 3.1 Å, cryo-EM structure of HIV-1 BG505DS-SOSIP.664 env trimer bound to DJ85-b.01 FAB

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