9Y9V: Rhesus macaque 1A8 and PGT121 fabs

The cryoem structure of rhesus macaque 1A8 and PGT121 fabs in complex with BG505 SOSIP.664. Determined by electron microscopy at 2.98 Å resolution. Released 27 May 2026.

Method: Electron microscopy
Resolution: 2.98 Å
Organisms: Human immunodeficiency virus 1, Macaca mulatta, Homo sapiens
Chains: 18
Atoms: 25,941
Mol. weight: 455.96 kDa
Ligands: NAG
Released: 27 May 2026

Explore 9Y9V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Y9V contains 78 α-helices and 266 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: 11 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	25
β-strand	45-47	3	26
β-strand	53-54	2	27
α-helix	58-62	5
β-strand	67	1	28
α-helix	75-78	4
β-strand	83-84	2	26
β-strand	91-94	4	29
α-helix	102-115	14
β-strand	121	1	30
α-helix	123-125	3
β-strand	129-133	5	31
β-strand	154-162	9	31
β-strand	169-177	9	31
α-helix	178-180	3
β-strand	181-183	3	31
β-strand	190-193	4	31
β-strand	200-203	4	30
α-helix	204-205	2
β-strand	209	1	28
β-strand	215	1	32
β-strand	217-218	2	27
β-strand	223-228	6	26
β-strand	236-239	4	29
β-strand	242-245	4	26
β-strand	247	1	27
β-strand	251	1	32
β-strand	261	1	33
β-strand	271-273	3	33
β-strand	284-312	27	33
β-strand	315-322	9	33
β-strand	329-334	6	33
α-helix	335-353	19
β-strand	358-361	4	33
α-helix	369-372	4
β-strand	374-378	5	33
β-strand	381-385	5	33
β-strand	393-395	3	33
β-strand	413-421	9	33
β-strand	423-424	2	30
α-helix	426-428	3
β-strand	432-435	4	30
α-helix	436-440	5
β-strand	441-457	17	33
β-strand	465-470	6	33
α-helix	477-480	4
β-strand	488-491	4	26
β-strand	495-497	3	25

Chain B: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	516-519	4
α-helix	530-533	4
α-helix	538-541	4
α-helix	570-594	25
β-strand	603-609	7	1
α-helix	610-611	2
α-helix	612-615	4
α-helix	619-621	3
α-helix	628-634	7
α-helix	641-662	22

Chain C: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	516-519	4
α-helix	530-533	4
α-helix	538-541	4
α-helix	570-594	25
β-strand	603-609	7	25
α-helix	612-615	4
α-helix	619-621	3
α-helix	628-634	7
α-helix	641-662	22

Chain d: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	40
β-strand	19-24	6	40
β-strand	33-38	6	41
β-strand	39	1	42
β-strand	46-51	6	41
β-strand	67-72	6	40
β-strand	77-82	6	40
β-strand	88-90	3	42
β-strand	92-97	6	41
β-strand	100-100A	2	43
α-helix	100E-100G	3
β-strand	100J-100K	2	43
β-strand	100N-100P	3	41
β-strand	105-107	3	42

Chain D: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	34
β-strand	17-18	2	35
β-strand	21-25	5	34
β-strand	34-39	7	36
β-strand	45-52	8	36
β-strand	57-59	3	36
α-helix	61-63	3
β-strand	70-72	3	37
β-strand	77-79	3	37
β-strand	82-82A	2	35
α-helix	84-86	3
β-strand	89-95	7	36
β-strand	103	1	36
β-strand	107-108	2	36

Chains e and m: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	44
β-strand	19-23	5	45
β-strand	31	1	46
β-strand	34-37	4	47
β-strand	38	1	44
β-strand	39	1	47
β-strand	42-48	7	47
β-strand	63	1	45
β-strand	71-75	5	45
α-helix	80-82	3
β-strand	85-86	2	44
β-strand	88-89	2	47
β-strand	92	1	46
α-helix	95A-95B	2
β-strand	97	1	41
β-strand	102-106	5	44

Chain E: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	38
β-strand	10-12	3	39
β-strand	19-25	7	38
β-strand	33-38	6	39
β-strand	45-49	5	39
β-strand	53-54	2	39
β-strand	63-65	3	38
β-strand	70-75	6	38
α-helix	80-82	3
β-strand	85-90	6	39
β-strand	97-98	2	39
β-strand	102-105	4	39

Chain G: 13 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	1
β-strand	45-47	3	2
β-strand	53-56	4	3
α-helix	59-62	4
β-strand	67	1	4
β-strand	75-76	2	3
α-helix	77-78	2
β-strand	83-84	2	2
β-strand	91-94	4	5
α-helix	102-115	14
β-strand	121	1	6
α-helix	123-125	3
β-strand	129-133	5	7
β-strand	154-162	9	7
β-strand	169-177	9	7
α-helix	178-180	3
β-strand	181-183	3	7
β-strand	190-193	4	7
α-helix	194-196	3
β-strand	200-203	4	6
α-helix	204-205	2
β-strand	209	1	4
β-strand	215	1	8
β-strand	216-218	3	3
β-strand	223-228	6	2
β-strand	236-239	4	5
β-strand	242-245	4	2
β-strand	247	1	3
β-strand	251	1	8
β-strand	261	1	9
α-helix	270	1
β-strand	271-273	3	9
β-strand	284-312	27	9
β-strand	315-322	9	9
β-strand	329-334	6	9
α-helix	335-353	19
β-strand	358-361	4	9
α-helix	369-372	4
β-strand	374-378	5	9
β-strand	381-385	5	9
β-strand	393-395	3	9
β-strand	413-421	9	9
β-strand	423-424	2	6
α-helix	426-428	3
β-strand	432-435	4	6
α-helix	436-440	5
β-strand	441-457	17	9
β-strand	465-470	6	9
α-helix	477-480	4
β-strand	488-491	4	2
β-strand	495-497	3	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
1A8 Fab heavy chain	D, H, K	protein	115	Macaca mulatta
1A8 Fab light chain	E, L, M	protein	106	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

>9Y9V_1 BG505 SOSIP.664 gp41 (chains B, C, J)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

>9Y9V_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

>9Y9V_3 1A8 Fab heavy chain (chains D, H, K)
QVQLQESGPGLVKPSETLSLTCSVSGGSVSEDHYWHWIRQAPGKGLEWIGFVYGSGVGSK
YNSSFQNRVTISLDTSKNQFSLTLNSMTAADTAVYYCARSPTGSWGQGLLVTVSS

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

>9Y9V_4 1A8 Fab light chain (chains E, L, M)
DIVMTQSPSSLSASVGDTVSMTCRASQGISSYLSWYQQKPGKAPRLLIFYANRLETGVPS
RFSGSGFGTEFTLTINSLQPEDSATYYCLQYHSLFTFGPGTKLDIN

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

>9Y9V_5 PGT121 Fab heavy chain (chains d, h, k)
QMQLQESGPGLVKPSETLSLTCSVSGASISDSYWSWIRRSPGKGLEWIGYVHKSGDTNYS
PSLKSRVNLSLDTSKNQVSLSLVAATAADSGKYYCARTLHGRRIYGIVAFNEWFTYFYMD
VWGNGTQVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

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

>9Y9V_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	18

Primary citation

THE CRYOEM STRUCTURE OF RHESUS MACAQUE 1A8 AND PGT121 FABS IN COMPLEX WITH BG505 SOSIP.664. Tolbert, W.D., Pozharski, E., 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,…
9Q0W 3.0 Å, Cryo-EM Structure of HIV-1 BG505DS-SOSIP.664 Env Trimer Bound to DFPH-a.01_10R59P_LC Fab
9Q3S 3.01 Å, Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 Fab in complex with HIV-1 Env…
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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